A container of Residues and the kinematics to manage them. More...
#include <Conformation.hh>
Public Member Functions | |
| 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 Conformation & | operator= (Conformation const &src) |
| equals operator 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... | |
| virtual ConformationOP | clone () const |
| clone the conformation 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... | |
| virtual bool | same_type_as_me (Conformation const &other, bool const recurse=true) const |
| determine the type of the ConformationOP 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... | |
| virtual void | chain_endings (utility::vector1< Size > const &endings) |
| Sets the list of (chain number) chain endings. More... | |
| virtual void | insert_chain_ending (Size const seqpos) |
| Marks <seqpos> as the end of a new (chain number) chain. More... | |
| virtual void | delete_chain_ending (Size const seqpos) |
| Deletes <seqpos> from the list of (chain number) chain endings. More... | |
| virtual void | reset_chain_endings () |
| Resets chain data so that the Conformation is marked as a single (chain number) chain. More... | |
| virtual void | chains_from_termini () |
| Rederive the (chain number) chains from the termini/polymer status. More... | |
| char | secstruct (Size seqpos) const |
| Returns the secondary structure the position <seqpos> More... | |
| virtual void | set_secstruct (Size const seqpos, char const setting) |
| Sets the secondary structure of the position <seqpos> to <setting> 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... | |
| virtual void | fold_tree (FoldTree const &fold_tree_in) |
| Sets the FoldTree to <fold_tree_in> 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... | |
| virtual void | append_residues (utility::vector1< conformation::ResidueOP > const &residues, utility::vector1< core::Size > const &jump_connection) |
| Function for building poses Append all the residues to the Conformation. If the corresponding jump connection is zero, attach by polymeric connection to the previous residue. More... | |
| virtual void | append_residue_by_jump (conformation::Residue const &new_rsd, Size const anchor_residue, std::string const &anchor_atom="", std::string const &root_atom="", bool const start_new_chain=false) |
| Append a new residue by a jump. 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 void | append_polymer_residue_after_seqpos (Residue const &new_rsd, Size const seqpos, bool const build_ideal_geometry) |
| glues to seqpos and perhaps also seqpos+1 More... | |
| virtual void | safely_append_polymer_residue_after_seqpos (Residue const &new_rsd, Size const seqpos, bool const build_ideal_geometry) |
| glues to seqpos and perhaps also seqpos+1, removes termini variants if necessary More... | |
| virtual void | prepend_polymer_residue_before_seqpos (Residue const &new_rsd, Size const seqpos, bool const build_ideal_geometry) |
| glues to seqpos and perhaps also seqpos-1 More... | |
| virtual void | safely_prepend_polymer_residue_before_seqpos (Residue const &new_rsd, Size const seqpos, bool const build_ideal_geometry) |
| glues to seqpos and perhaps also seqpos-1, removes termini variants if necessary More... | |
| virtual void | replace_residue (Size const seqpos, Residue const &new_rsd, bool const orient_backbone) |
| replace residue More... | |
| virtual void | replace_residue (Size const seqpos, Residue const &new_rsd, utility::vector1< std::pair< std::string, std::string > > const &atom_pairs) |
| function to replace a residue based on superposition on the specified input atom pairs More... | |
| virtual void | delete_polymer_residue (Size const seqpos) |
| Delete polymer residue at the given sequence position. More... | |
| virtual void | delete_residue_slow (Size const seqpos) |
| Slow method that relies on FoldTree::delete_seqpos, rebuilds atomtree, can handle jumps/root residue. More... | |
| virtual void | delete_residue_range_slow (Size const range_begin, Size const range_end) |
| Slow method that relies on FoldTree::delete_seqpos, rebuilds atomtree, can handle jumps/root residue. 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... | |
| virtual void | declare_chemical_bond (Size const seqpos1, std::string const &atom_name1, Size const seqpos2, std::string const &atom_name2) |
| Declare that a chemical bond exists between two residues. 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... | |
| virtual void | rebuild_polymer_bond_dependent_atoms (Size const seqpos) |
| Rebuild the atoms ( like HN(seqpos), OC(seqpos+1) ) that are dependent on the polymer bond between seqpos and seqpos+1. 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... | |
| virtual void | fill_missing_atoms (id::AtomID_Mask missing) |
| bool | atom_is_backbone_norefold (Size pos, Size atomno) const |
| returns true if atom is part of backbone. More... | |
| virtual void | set_stub_transform (id::StubID const &stub_id1, id::StubID const &stub_id2, kinematics::RT const &target_rt) |
| Set the transform between two stubs – only works if there's a jump between the two sets of stubatoms. 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... | |
| virtual void | set_polymeric_connection (Size res_id_lower, Size res_id_upper) |
| identify polymeric connections 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< std::pair< Size, Size > > const &disulfs) |
| Detect existing disulfides from the protein structure, using the provided pairs as a starting point. More... | |
| void | detect_disulfides () |
| Detect existing disulfides from the protein structure. More... | |
| virtual void | fix_disulfides (utility::vector1< std::pair< Size, Size > > const &disulf_bonds) |
| Assigns disulfide bonds based on a pre-determined list. More... | |
| virtual bool | add_disulfide_bond (core::Size res1, core::Size res2) |
| Attempt to add a disulfide bond between the two residues. Returns true on success and false on failure. 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... | |
| virtual void | insert_conformation_by_jump (Conformation const &conf, Size const insert_seqpos, Size const insert_jumppos, Size const anchor_pos, Size const anchor_jump_number=0, std::string const &anchor_atom="", std::string const &root_atom="") |
| Insert one conformation into another. See FoldTree::insert_fold_tree_by_jump. More... | |
| void | copy_segment (Size size, Conformation const &src, Size begin, Size src_begin) |
| copy a stretch of coordinates/torsions from another Conformation More... | |
| virtual void | insert_fragment (id::StubID const &instub_id, FragRT const &outstub_transforms, FragXYZ const &frag_xyz) |
| Real | dof (DOF_ID const &id) const |
| Returns the AtomTree degree of freedom (DOF) <id> More... | |
| virtual void | set_dof (DOF_ID const &id, Real const setting) |
| Sets the AtomTree degree of freedom (DOF) <id> to <setting> More... | |
| Real | torsion (TorsionID const &id) const |
| Return the torsion angle OR rigid-body offset for <id> More... | |
| virtual void | set_torsion (TorsionID const &id, Real const setting) |
| Sets the AtomTree DOF and the torsion OR rigid-body offset in the corresponding Residue or Jump. 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... | |
| virtual void | set_torsion_angle (AtomID const &atom1, AtomID const &atom2, AtomID const &atom3, AtomID const &atom4, Real const setting, bool const quiet=false) |
| Sets the torsion angle defined by <atom[1-4]> to <setting> 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... | |
| virtual void | set_bond_angle (AtomID const &atom1, AtomID const &atom2, AtomID const &atom3, Real const setting) |
| Sets the bond angle defined by <atom[1-3]> to <setting> More... | |
| Real | bond_length (AtomID const &atom1, AtomID const &atom2) const |
| Returns the bond length between <atom1> and <atom2> through the AtomTree. More... | |
| virtual void | set_bond_length (AtomID const &atom1, AtomID const &atom2, Real const setting) |
| Sets the cond length between <atom1> and <atom2> to <setting> 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... | |
| virtual void | set_jump (int const jump_number, Jump const &new_jump) |
| Sets the jump <jump_number> to <new_jump> More... | |
| virtual void | set_jump (AtomID const &id, Jump const &new_jump) |
| set 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) |
| virtual void | insert_ideal_geometry_at_polymer_bond (Size const seqpos) |
| virtual void | insert_ideal_geometry_at_residue_connection (Size const pos1, Size const connid1) |
| 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... | |
| virtual void | reset_move_data () |
| forget all the structure modifications 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... | |
| virtual void | push_passport (core::environment::DofPassportCOP) |
| virtual core::environment::DofPassportCOP | pop_passport () |
| virtual bool | has_passport () const |
| virtual bool | is_protected () const |
| 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... | |
Protected Member Functions | |
| 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... | |
Private Member Functions | |
| Residue & | residue_ (Size seqpos) |
| Returns a non-constant residue reference without triggering coordinate/torsion update. More... | |
| void | update_sequence_numbering (Size new_size, utility::vector1< Size > const &old2new) |
| remap *_moved arrays, sequence numbering in the residues_ arrays, etc, after insertion or deletion of rsds More... | |
| void | rebuild_polymer_bond_dependent_atoms (Size const seqpos, int const upper_lower) |
| rebuild atoms in residue seqpos dependent on either the lower (-1) or upper(1) polymer residue More... | |
| void | insert_polymer_residue (Residue const &new_rsd_in, Size const seqpos, bool const join_lower, bool const join_upper) |
| void | append_residue (Residue const &new_rsd_in, bool const attach_by_jump, std::string const &root_atom, id::NamedAtomID anchor_id, bool const start_new_chain, bool const skip_atomtree=false) |
| Now a private method public interface: append_residue_by_bond or append_residue_by_jump. More... | |
| void | residues_replace (Size seqpos, Residue const &new_rsd) |
| wrap direct access to the Residues container More... | |
| void | residues_insert (Size seqpos, Residue const &new_rsd, bool use_lower_chain=false, bool new_chain=false) |
| void | residues_append (Residue const &new_rsd, bool start_new_chain, bool by_jump=false, std::string const &root_atom="", id::NamedAtomID anchor_id=id::NamedAtomID::BOGUS_NAMED_ATOM_ID()) |
| void | residues_delete (Size seqpos) |
| void | setup_atom_tree () |
| (re-)builds the AtomTree using the FoldTree and the Residues More... | |
| Real | atom_tree_torsion (TorsionID const &tor_id) const |
| access a torsion from the atom_tree More... | |
| bool | backbone_torsion_angle_atoms_oligourea (TorsionID const &id, AtomID &id1, AtomID &id2, AtomID &id3, AtomID &id4) const |
| Get four backbone atoms which define this backbone torsion, if this residue is an oligourea. More... | |
| bool | backbone_torsion_angle_atoms_ortho_aramid (TorsionID const &id, AtomID &id1, AtomID &id2, AtomID &id3, AtomID &id4) const |
| Get four backbone atoms which define this backbone torsion, if this residue is an aramid. More... | |
| bool | backbone_torsion_angle_atoms_meta_aramid (TorsionID const &id, AtomID &id1, AtomID &id2, AtomID &id3, AtomID &id4) const |
| Get four backbone atoms which define this backbone torsion, if this residue is an aramid. More... | |
| bool | backbone_torsion_angle_atoms_para_aramid (TorsionID const &id, AtomID &id1, AtomID &id2, AtomID &id3, AtomID &id4) const |
| Get four backbone atoms which define this backbone torsion, if this residue is an aramid. More... | |
| bool | branch_connection_torsion_angle_atoms (TorsionID const &torsion, AtomID &id1, AtomID &id2, AtomID &id3, AtomID &id4) const |
| Find the four atoms that define the torsion angle of this branch connection. More... | |
| void | set_xyz_moved (AtomID const &id) |
| notify of xyz-change More... | |
| void | set_xyz_moved (utility::vector1< AtomID > const &ids) |
| notify of mutiple-xyz-change More... | |
| void | set_dof_moved (AtomID const &id) |
| notify of dof-change More... | |
| void | set_dof_moved (DOF_ID const &id) |
| notify of dof-change More... | |
| void | update_residue_coordinates () const |
| Will (if necessary) copy the xyz coordinates from the AtomTree to the Residues being managed. More... | |
| void | update_residue_coordinates (Size seqpos, bool fire_signal=true) const |
| void | rederive_chain_endings () |
| void | rederive_chain_ids () |
| void | update_residue_torsions () const |
| Will (if necessary) copy the torsion angles (mainchain/chi) from the AtomTree to the Residues being managed. More... | |
| void | update_residue_torsions (Size seqpos, bool fire_signal=true) const |
| void | add_pseudobond (Size lr, Size lr_connid, Size ur, Size ur_connid, Size nbonds) |
| void | in_place_copy (Conformation const &src) |
| Optimizing the common case of assigning a conformation to another with the same sequence. More... | |
| void | pre_nresidue_change () |
| The Conformation must transfer lazily accumulated "moved" data from the AtomTree before changing the number of residues. More... | |
| void | notify_connection_obs (ConnectionEvent const &e) const |
| notify ConnectionEvent observers More... | |
| void | notify_general_obs (GeneralEvent const &e) const |
| notify GeneralEvent observers More... | |
| void | notify_identity_obs (IdentityEvent const &e, bool fire_general=true) const |
| notify IdentityEvent observers More... | |
| void | notify_length_obs (LengthEvent const &e, bool fire_general=true) const |
| notify LengthEvent observers More... | |
| void | notify_xyz_obs (XYZEvent const &e, bool fire_general=true) const |
| notify XYZEvent observers More... | |
Private Attributes | |
| ResidueOPs | residues_ |
| container of Residues More... | |
| core::chemical::CacheableResidueTypeSets | residue_type_sets_ |
| Any Conformation-specific ResidueTypes are stored here. Note: The ResidueTypeSets contained herein can be shared by multiple Conformations, and should have copy-on-write semantics. More... | |
| utility::vector1< Size > | chain_endings_ |
| chain number for each position More... | |
| FoldTreeOP | fold_tree_ |
| fold tree for the kinematics More... | |
| AtomTreeOP | atom_tree_ |
| atom tree for the kinematics More... | |
| membrane::MembraneInfoOP | membrane_info_ |
| Membrane Info object. More... | |
| carbohydrates::GlycanTreeSetObserverOP | tree_set_observer_ = nullptr |
| GlycanTreeSetObserver Object. More... | |
| utility::vector1< ParametersSetOP > | parameters_set_ |
| Parameter sets for parametric conformation generation. More... | |
| bool | contains_carbohydrate_residues_ |
| bool | residue_coordinates_need_updating_ |
| do we need to update the coordinates in the Residues? More... | |
| bool | residue_torsions_need_updating_ |
| do we need to update the torsion angles in the Residues? More... | |
| AtomID_Mask | dof_moved_ |
| book-keeping array for energy evaluations More... | |
| AtomID_Mask | xyz_moved_ |
| book-keeping array for energy evaluations More... | |
| bool | structure_moved_ |
| has the structure moved since the last call to reset_move_data? More... | |
| utility::vector1< char > | secstruct_ |
| utility::signals::BufferedSignalHub< void, ConnectionEvent > | connection_obs_hub_ |
| ConnectionEvent observers. More... | |
| utility::signals::PausableSignalHub< void, GeneralEvent > | general_obs_hub_ |
| GeneralEvent observers. More... | |
| utility::signals::BufferedSignalHub< void, IdentityEvent > | identity_obs_hub_ |
| IdentityEvent observers. More... | |
| utility::signals::BufferedSignalHub< void, LengthEvent > | length_obs_hub_ |
| LengthEvent observers. More... | |
| utility::signals::BufferedSignalHub< void, XYZEvent > | xyz_obs_hub_ |
| LengthEvent observers. More... | |
Friends | |
| class | ::ConformationTests |
Detailed Description
A container of Residues and the kinematics to manage them.
Member Typedef Documentation
◆ AtomID
◆ AtomID_Mask
◆ AtomTree
◆ AtomTreeOP
◆ ConnectionEvent
| typedef core::conformation::signals::ConnectionEvent core::conformation::Conformation::ConnectionEvent |
◆ const_iterator
| typedef boost::indirect_iterator< ResidueOPs::const_iterator, Residue const > core::conformation::Conformation::const_iterator |
◆ difference_type
| typedef ptrdiff_t core::conformation::Conformation::difference_type |
◆ DOF_ID
◆ DomainMap
◆ FoldTree
◆ FoldTreeOP
◆ FragRT
| typedef std::map< id::StubID, kinematics::RT > core::conformation::Conformation::FragRT |
◆ FragXYZ
| typedef std::map< id::AtomID, Vector > core::conformation::Conformation::FragXYZ |
◆ GeneralEvent
◆ IdentityEvent
◆ iterator
| typedef boost::indirect_iterator< ResidueOPs::iterator, Residue const > core::conformation::Conformation::iterator |
◆ Jump
◆ LengthEvent
◆ Parameters
◆ ParametersCOP
| typedef core::conformation::parametric::ParametersOP core::conformation::Conformation::ParametersCOP |
◆ ParametersOP
◆ ParametersSet
| typedef core::conformation::parametric::ParametersSet core::conformation::Conformation::ParametersSet |
◆ ParametersSetCOP
| typedef core::conformation::parametric::ParametersSetCOP core::conformation::Conformation::ParametersSetCOP |
◆ ParametersSetOP
| typedef core::conformation::parametric::ParametersSetOP core::conformation::Conformation::ParametersSetOP |
◆ PartialAtomID
◆ size_type
◆ TorsionID
◆ XYZEvent
Constructor & Destructor Documentation
◆ Conformation() [1/2]
| core::conformation::Conformation::Conformation | ( | ) |
◆ ~Conformation()
|
override |
default destructor
◆ Conformation() [2/2]
| core::conformation::Conformation::Conformation | ( | Conformation const & | src | ) |
copy constructor
References atom_tree_, chain_endings_, contains_carbohydrate_residues_, dof_moved_, fold_tree_, membrane_info_, parameters_set_, residue_coordinates_need_updating_, residue_torsions_need_updating_, residue_type_sets_, residues_, secstruct_, size(), structure_moved_, tree_set_observer_, and xyz_moved_.
Member Function Documentation
◆ aa()
|
inline |
Returns the AA enum for position <seqpos>
References residues_, and size().
Referenced by core::conformation::symmetry::SymmetricConformation::get_upstream_vrt(), and core::conformation::symmetry::SymmetricConformation::recalculate_transforms().
◆ add_disulfide_bond()
|
virtual |
Attempt to add a disulfide bond between the two residues. Returns true on success and false on failure.
References core::conformation::change_cys_state(), declare_chemical_bond(), core::chemical::DISULFIDE, core::chemical::ResidueTypeBase::get_disulfide_atom_name(), residue_type(), residues_, size(), core::id::to_string(), and core::conformation::TR().
Referenced by detect_disulfides(), core::conformation::symmetry::SymmetricConformation::detect_disulfides(), and fix_disulfides().
◆ add_parameters_set()
| void core::conformation::Conformation::add_parameters_set | ( | ParametersSetOP | newset | ) |
Add a (predefined) ParametersSet object (via its owning pointer) to the current Conformation object.
References parameters_set_.
Referenced by protocols::helical_bundle::MakeBundleHelix::add_parameter_info_to_pose(), protocols::helical_bundle::MakeBundle::apply(), and insert_conformation_by_jump().
◆ add_pseudobond()
◆ align_virtual_atoms_in_carbohydrate_residue()
| void core::conformation::Conformation::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.
This method aligns virtual atom VOX, where X is the position of the cyclic oxygen, OY and HOY, where Y is the position of the anomeric carbon, (provided the residue is not the reducing end, where OY and HOY would be real atoms), and HOZ, where Z is the mainchain glycosidic bond location. OY and HOY are aligned with the last two "main chain" atoms of the parent residue. This ensures that torsion angles with duplicate names, e.g., chi1 and phi for internal linked aldoses, will always return the same values. The same concept applies for HOZ, which aligns with the anomeric carbon of the downstream residue. This method should be called after any coordinate change for a sac- charide residue and after loading a saccharide residue from a file or sequence for the first time.
- Note
- Do I need to worry about aligning the virtual atoms left over from modified sugar patches? Can such virtual atoms be deleted?
References core::conformation::Residue::atom_index(), core::conformation::Residue::atom_name(), core::conformation::Residue::carbohydrate_info(), core::conformation::Residue::connect_atom(), core::conformation::carbohydrates::find_seqpos_of_saccharides_parent_residue(), core::conformation::Residue::first_adjacent_heavy_atom(), core::conformation::Residue::is_lower_terminus(), core::conformation::Residue::is_upper_terminus(), core::chemical::ResidueType::residue_connection_id_for_atom(), core::conformation::Residue::residue_connection_partner(), residues_, set_xyz(), core::conformation::TR(), core::conformation::Residue::type(), and xyz().
Referenced by set_bond_angle(), set_bond_length(), and set_torsion_angle().
◆ annotated_sequence()
| std::string core::conformation::Conformation::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].
References core::conformation::Residue::annotated_name(), residue(), and size().
Referenced by fold_tree().
◆ append_polymer_residue_after_seqpos()
|
virtual |
glues to seqpos and perhaps also seqpos+1
Fires a LengthEvent::RESIDUE_PREPEND signal at seqpos + 1 due to insert_polymer_residue() call.
Reimplemented in protocols::environment::ProtectedConformation, and core::conformation::symmetry::SymmetricConformation.
References core::conformation::Residue::clone(), dof_moved_, fold_tree_, insert_polymer_residue(), core::conformation::Residue::is_lower_terminus(), core::conformation::Residue::is_upper_terminus(), core::conformation::Residue::lower_connect(), core::conformation::Residue::natoms(), core::conformation::orient_residue_for_ideal_bond(), pre_nresidue_change(), rebuild_polymer_bond_dependent_atoms(), residue_(), residue_coordinates_need_updating_, size(), core::id::AtomID_Map< T >::size(), update_residue_coordinates(), core::conformation::Residue::upper_connect(), and xyz_moved_.
Referenced by protocols::chemically_conjugated_docking::add_extra_bodies(), core::conformation::symmetry::SymmetricConformation::append_polymer_residue_after_seqpos(), protocols::protein_interface_design::movers::LoopLengthChange::apply(), core::conformation::idealize_position(), core::conformation::insert_ideal_bonds_at_polymer_junction(), core::conformation::insert_ideal_mainchain_bonds(), protocols::rna::movers::RNAThreadAndMinimizeMover::process_insertions(), and safely_append_polymer_residue_after_seqpos().
◆ append_residue()
|
private |
Now a private method public interface: append_residue_by_bond or append_residue_by_jump.
add a residue into residues_ container, update its seqpos, chainid as well fold tree and atoms. private now – this is our internal routine with everything determined ahead of time root_atomno and anchor_id.atomno() may not be filled in yet Fires a LengthEvent::RESIDUE_APPEND signal.
References core::id::NamedAtomID::atom(), core::conformation::Residue::atom_index(), atom_tree_, const_residues(), contains_carbohydrate_residues_, fold_tree_, core::conformation::Residue::has_lower_connect(), core::conformation::insert_residue_into_atom_tree(), core::chemical::ResidueType::is_carbohydrate(), core::conformation::Residue::is_ligand(), core::conformation::Residue::is_lower_terminus(), core::conformation::Residue::lower_connect_atom(), core::conformation::Residue::name(), notify_length_obs(), pre_nresidue_change(), core::conformation::signals::LengthEvent::RESIDUE_APPEND, residue_torsions_need_updating_, residues_, residues_append(), core::id::NamedAtomID::rsd(), setup_atom_tree(), size(), core::conformation::TR(), and core::conformation::Residue::type().
Referenced by append_residue_by_bond(), append_residue_by_jump(), and append_residues().
◆ append_residue_by_bond()
| void core::conformation::Conformation::append_residue_by_bond | ( | conformation::Residue const & | new_rsd, |
| bool const | build_ideal_geometry = false, |
||
| int | residue_connection_index = 0, |
||
| Size | anchor_pos = 0, |
||
| int | anchor_residue_connection_index = 0, |
||
| bool const | start_new_chain = false, |
||
| bool const | lookup_bond_length = false |
||
| ) |
Append a new residue by a bond.
The default behavior is to append by a polymeric connection to the preceding residue If we want to connect via a non-polymer connection, we give the connection number, anchor residue and the connection number for the anchor residue. These connection numbers are wrt the connections_ arrays in Residue and ResidueType If build_ideal_bond is TRUE it will transform the coordinates of the new residue so that the bond geometry of the new bond is ideal according to the icoor_internal data in the residues. Otherwise the incoming coordinates of new_rsd are preserved. Fires a LengthEvent::RESIDUE_APPEND signal.
References append_residue(), core::conformation::atom_id_to_named_atom_id(), core::conformation::Residue::atom_name(), core::chemical::ResidueConnection::atomno(), core::id::AtomID::atomno(), core::id::NamedAtomID::BOGUS_NAMED_ATOM_ID(), core::conformation::Residue::clone(), core::conformation::Residue::is_polymer(), core::conformation::Residue::lower_connect(), core::conformation::Residue::lower_connect_atom(), core::chemical::ResidueType::lower_connect_id(), core::chemical::ResidueTypeBase::name(), core::conformation::orient_residue_for_ideal_bond(), pre_nresidue_change(), rebuild_polymer_bond_dependent_atoms(), residue_(), core::conformation::Residue::residue_connection(), residue_coordinates_need_updating_, residues_, size(), core::conformation::Residue::type(), update_residue_coordinates(), core::conformation::Residue::upper_connect(), core::conformation::Residue::upper_connect_atom(), and core::chemical::ResidueType::upper_connect_id().
Referenced by protocols::loops::loop_closure::kinematic_closure::KinematicMover::apply(), protocols::comparative_modeling::ExtraThreadingMover::apply(), core::conformation::idealize_position(), core::conformation::insert_ideal_bonds_at_polymer_junction(), core::conformation::insert_ideal_mainchain_bonds(), and core::conformation::is_ideal_position().
◆ append_residue_by_jump()
|
virtual |
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 in protocols::environment::ProtectedConformation, core::conformation::symmetry::SymmetricConformation, and core::conformation::symmetry::MirrorSymmetricConformation.
References append_residue(), core::id::NamedAtomID::BOGUS_NAMED_ATOM_ID(), pre_nresidue_change(), and size().
Referenced by protocols::chemically_conjugated_docking::add_extra_bodies(), protocols::loop_grower::LoopPartialSolution::add_sheets(), protocols::environment::EnvClaimBroker::add_virtual_residues(), protocols::loop_grower::SheetSampler::apply(), protocols::comparative_modeling::ExtraThreadingMover::apply(), protocols::simple_filters::SSMotifFinder::compute_jump(), and core::conformation::symmetry::setup_symmetric_conformation().
◆ append_residues()
|
virtual |
Function for building poses Append all the residues to the Conformation. If the corresponding jump connection is zero, attach by polymeric connection to the previous residue.
References append_residue(), core::conformation::atom_id_to_named_atom_id(), core::conformation::Residue::atom_name(), core::id::NamedAtomID::BOGUS_NAMED_ATOM_ID(), core::conformation::Residue::has_lower_connect(), core::conformation::Residue::has_upper_connect(), core::conformation::Residue::lower_connect_atom(), core::chemical::ResidueType::lower_connect_id(), core::chemical::ResidueTypeBase::name(), notify_length_obs(), pre_nresidue_change(), residue_(), core::conformation::signals::LengthEvent::RESIDUE_APPEND, residues_, setup_atom_tree(), size(), core::conformation::Residue::type(), core::conformation::Residue::upper_connect_atom(), and core::chemical::ResidueType::upper_connect_id().
◆ apply_transform_Rx_plus_v()
|
virtual |
Reimplemented in core::conformation::symmetry::SymmetricConformation.
References batch_set_xyz(), core::conformation::Residue::natoms(), residue_(), size(), and xyz().
◆ atom_is_backbone_norefold()
returns true if atom is part of backbone.
There is a version of this in Residue.hh. The problem with that function is that accessing a residue in the pose triggers a refold which is really slow. We do not need a correctly folded residue to makethis check
References residues_.
Referenced by core::conformation::symmetry::guess_torsion_type_of_dof_id().
◆ atom_tree()
|
inline |
Returns the conformation's AtomTree.
References atom_tree_.
Referenced by protocols::simple_filters::JumpEvaluator::apply(), protocols::environment::collect_dofs(), protocols::simple_filters::SimpleHbondsToAtomFilter::compute(), core::energy_methods::LinearChainbreakEnergy::do_score_ovp(), protocols::abinitio::abscript::fix_internal_coords_of_siblings(), protocols::topology_broker::fix_internal_coords_of_siblings(), core::conformation::is_ideal_position(), protocols::simple_filters::JumpEvaluator::JumpEvaluator(), core::optimization::CartesianMinimizerMap::setup(), core::optimization::MinimizerMap::setup(), core::optimization::symmetry::SymMinimizerMap::SymMinimizerMap(), core::kinematics::jacobian::ModuleType1::update_screw_vectors(), and protocols::environment::claims::XYZClaim::yield_elements().
◆ atom_tree_torsion()
access a torsion from the atom_tree
used when we want to copy torsions from the atomtree to the residues used when updating the torsion angles stashed in the Residues other torsion access calls look inside the residues since this will be faster than getting from the atomtree, at least in the current implementation of this routine
References atom_tree_, core::id::AtomID::atomno(), atoms_are_bonded(), const_residue_(), dof_id_from_torsion_id(), get_torsion_angle_atom_ids(), core::id::JUMP, core::id::AtomID::rsd(), core::id::TorsionID::type(), and core::conformation::Residue::xyz().
Referenced by debug_residue_torsions(), and update_residue_torsions().
◆ atoms_are_bonded()
| bool core::conformation::Conformation::atoms_are_bonded | ( | AtomID const & | id1, |
| AtomID const & | id2 | ||
| ) | const |
Helper method to determine whether two atoms have a chemical bond linking them.
Helper function to determine whether two atoms have a chemical bond linking them.
Intended for internal use, but there's really no reason not to make this a public method. This works for atoms within the same residue or in different residues. AMW went and made this a public method.
References core::id::AtomID::atomno(), core::chemical::ResidueType::atoms_are_bonded(), core::conformation::Residue::connected_residue_at_resconn(), core::conformation::Residue::connections_to_residue(), const_residue_(), core::conformation::Residue::is_bonded(), core::conformation::Residue::residue_connect_atom_index(), core::conformation::Residue::residue_connection_conn_id(), core::id::AtomID::rsd(), and core::conformation::Residue::type().
Referenced by atom_tree_torsion(), protocols::rna::movers::atoms_have_bond_to_bonded_atoms(), protocols::rna::movers::atoms_have_mutual_bond_to_atom(), core::import_pose::build_pose_as_is2(), protocols::rna::movers::bump_check(), and torsion_angle().
◆ attach_connection_obs()
|
inline |
attach ConnectionEvent observer function
- Parameters
-
fn pointer to observer's unary member function with signature void( ConnectionEvent const & ) ptr RAW pointer to observer object
- Returns
- Link that can be used to manage the connection
- Remarks
- ConnectionEvent observers will only be notified upon a change in the state of the connection with the Conformation, e.g. if the Conformation is destroyed or if the connection is being transferred. SUGGESTION: Try to use the Link objects that are returned when attaching observers instead of attaching via this function and watching for ConnectionEvents, as it typically makes connection management easier.
References connection_obs_hub_.
Referenced by core::pose::PDBInfo::attach_to().
◆ attach_general_obs()
|
inline |
attach GeneralEvent observer function
- Parameters
-
fn pointer to observer's unary member function with signature void( GeneralEvent const & ) ptr RAW pointer to observer object
- Returns
- Link that can be used to manage the connection
- Remarks
- GeneralEvent observers will be notified whenever any signal derived from GeneralEvent occurs.
References general_obs_hub_.
◆ attach_identity_obs()
|
inline |
attach IdentityEvent observer function
- Parameters
-
fn pointer to observer's unary member function with signature void( IdentityEvent const & ) ptr RAW pointer to observer object
- Returns
- Link that can be used to manage the connection
References identity_obs_hub_.
Referenced by core::pose::PDBInfo::attach_to().
◆ attach_length_obs()
|
inline |
attach LengthEvent observer function
- Parameters
-
fn pointer to observer's unary member function with signature void( LengthEvent const & ) ptr RAW pointer to observer object
- Returns
- Link that can be used to manage the connection
References length_obs_hub_.
Referenced by core::conformation::carbohydrates::GlycanTreeSetObserver::attach_impl(), protocols::denovo_design::components::StructureDataObserver::attach_impl(), protocols::toolbox::match_enzdes_util::EnzdesCacheableObserver::attach_impl(), core::pose::datacache::LengthEventCollector::attach_impl(), core::pose::datacache::SpecialSegmentsObserver::attach_impl(), core::pose::PDBInfo::attach_to(), and protocols::forge::build::BuildInstruction::attach_to().
◆ attach_xyz_obs()
|
inline |
attach XYZEvent observer function
- Parameters
-
fn pointer to observer's unary member function with signature void( XYZEvent const & ) ptr RAW pointer to observer object
- Returns
- Link that can be used to manage the connection
References xyz_obs_hub_.
◆ backbone_torsion_angle_atoms()
| bool core::conformation::Conformation::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
- Note
- Returns TRUE to signal FAILURE
messy... could perhaps keep this cached if speed is an issue but then have to keep sync'ed with changes in the residues
I don't think this is going to be performance critical
consider that in current rosetta we routinely re-evaluate all the backbone and sidechain torsion angles from the xyz coordinates...
This was hacky to begin with, but I feel that I have made it more hacky now. I am currently working on a more elegent method to handle residue types that have a a non-standard number of backbone torsions (ie. beta-peptides, beta-peptoids, and the dipeptides ACE-X-NME I use for making rotamers) –Doug
Dear 2010 Doug, Sorry, I have completely forgoton what we were talking about in your comment. Very Fermat of you. I have a few vauge ideas about what this miraculous solution could possibly be but we probably had more brain cells then so who knows. Basically defining the atoms that comprise the backbone torsions in the params files themselves and storing that in the ResidueType, like is currently done for the chi angles. I guess it is just the cacheing idea in the comments before mine. That way, patches could modify which atoms make up backbone torsions and we would not need special if checks to look at varient types if we want to have 4 backbone torsions. Until then however I am just going to make this function more hacky, sorry. Love, 2012 Doug
Dear all Dougs, I am making this somewhat more elegant, maybe, at least for the ACE-X-NME case, because unless torsion is 1, ntorsions, or ntorsions-1 all the atoms are part of the mainchain Best, Andy
Dear Dougs & Andy, Thank you for a most enjoyable dialog. Sincerely, Labonte
Dear Dougs, Andy, and Jason:
It's 2018, now, and this is STILL a mess. We really should clean this up and have ResidueTypes properly cache their torsion IDs at some point. It's becoming more and more of a headache as we add more noncanonical types.
Sincerely, 2018 Vikram
P.S. 2017 Vikram: why didn't you insist on cleaning this up at the noncanonicals XRW? Head injury is no excuse!
- Note
- returns TRUE for FAILURE
References core::chemical::ACETYLATED_NTERMINUS_VARIANT, core::conformation::Residue::atom_index(), core::chemical::ICoorAtomID::atomno(), core::id::AtomID::atomno(), backbone_torsion_angle_atoms_meta_aramid(), backbone_torsion_angle_atoms_oligourea(), backbone_torsion_angle_atoms_ortho_aramid(), backbone_torsion_angle_atoms_para_aramid(), core::chemical::C_METHYLAMIDATION, core::conformation::Residue::connect_map_size(), core::conformation::Residue::connection_incomplete(), const_residue_(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::chemical::FIVE_PRIME_PHOSPHATE, fold_tree_, core::conformation::Residue::has_lower_connect(), core::conformation::Residue::has_upper_connect(), core::conformation::Residue::has_variant_type(), core::chemical::ResidueType::icoor(), core::chemical::ResidueType::is_aramid(), core::conformation::Residue::is_carbohydrate(), core::chemical::ResidueType::is_meta_aramid(), core::chemical::ResidueType::is_oligourea(), core::chemical::ResidueType::is_ortho_aramid(), core::chemical::ResidueType::is_para_aramid(), core::chemical::ResidueType::is_post_methylene_meta_aramid(), core::chemical::ResidueType::is_post_methylene_ortho_aramid(), core::chemical::ResidueType::is_post_methylene_para_aramid(), core::chemical::ResidueType::is_pre_methylene_meta_aramid(), core::chemical::ResidueType::is_pre_methylene_ortho_aramid(), core::chemical::ResidueType::is_pre_methylene_para_aramid(), core::chemical::ResidueType::is_pre_methylene_post_methylene_meta_aramid(), core::chemical::ResidueType::is_pre_methylene_post_methylene_ortho_aramid(), core::chemical::ResidueType::is_pre_methylene_post_methylene_para_aramid(), core::conformation::Residue::is_RNA(), core::chemical::ResidueType::lower_connect_id(), core::conformation::Residue::mainchain_atom(), core::conformation::Residue::mainchain_atoms(), core::conformation::Residue::mainchain_torsions(), core::chemical::METHYLATED_CTERMINUS_VARIANT, core::chemical::N_ACETYLATION, core::conformation::Residue::residue_connect_atom_index(), core::conformation::Residue::residue_connection_conn_id(), core::conformation::Residue::residue_connection_partner(), residues_, core::id::AtomID::rsd(), core::chemical::AtomICoor::stub_atom1(), core::chemical::THREE_PRIME_PHOSPHATE, torsion(), core::conformation::Residue::type(), and core::chemical::ResidueType::upper_connect_id().
Referenced by get_torsion_angle_atom_ids(), and protocols::helical_bundle_predict::HBPHelix::get_torsions_for_helix().
◆ backbone_torsion_angle_atoms_meta_aramid()
|
private |
Get four backbone atoms which define this backbone torsion, if this residue is an aramid.
References core::chemical::ACETYLATED_NTERMINUS_VARIANT, core::conformation::Residue::atom_index(), core::id::AtomID::atomno(), core::conformation::Residue::connect_map_size(), core::conformation::Residue::connected_residue_at_lower(), core::conformation::Residue::connected_residue_at_upper(), const_residue_(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::conformation::get_second_atom_from_connection(), core::conformation::Residue::has_lower_connect(), core::conformation::Residue::has_upper_connect(), core::conformation::Residue::has_variant_type(), core::chemical::ResidueType::is_aramid(), core::chemical::ResidueType::is_post_methylene_meta_aramid(), core::chemical::ResidueType::is_pre_methylene_meta_aramid(), core::chemical::ResidueType::is_pre_methylene_post_methylene_meta_aramid(), core::chemical::ResidueType::lower_connect_id(), core::chemical::METHYLATED_CTERMINUS_VARIANT, core::chemical::N_ACETYLATION, core::conformation::Residue::residue_connect_atom_index(), core::conformation::Residue::residue_connection_conn_id(), residues_, core::id::AtomID::rsd(), torsion(), core::conformation::Residue::type(), and core::chemical::ResidueType::upper_connect_id().
Referenced by backbone_torsion_angle_atoms().
◆ backbone_torsion_angle_atoms_oligourea()
|
private |
Get four backbone atoms which define this backbone torsion, if this residue is an oligourea.
I'm adding this function because backbone_torsion_angle_atoms() is an Escherian labyrinth.
References core::conformation::Residue::atom_index(), core::id::AtomID::atomno(), core::conformation::Residue::connect_map_size(), core::conformation::Residue::connected_residue_at_lower(), core::conformation::Residue::connected_residue_at_upper(), const_residue_(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::conformation::get_second_atom_from_connection(), core::conformation::Residue::has_lower_connect(), core::conformation::Residue::has_upper_connect(), core::conformation::Residue::has_variant_type(), core::chemical::ResidueType::is_oligourea(), core::chemical::ResidueType::lower_connect_id(), core::chemical::METHYLATED_CTERMINUS_VARIANT, core::chemical::N_ACETYLATION, core::conformation::Residue::residue_connect_atom_index(), core::conformation::Residue::residue_connection_conn_id(), residues_, core::id::AtomID::rsd(), torsion(), core::conformation::Residue::type(), and core::chemical::ResidueType::upper_connect_id().
Referenced by backbone_torsion_angle_atoms().
◆ backbone_torsion_angle_atoms_ortho_aramid()
|
private |
Get four backbone atoms which define this backbone torsion, if this residue is an aramid.
References core::conformation::Residue::atom_index(), core::id::AtomID::atomno(), core::conformation::Residue::connect_map_size(), core::conformation::Residue::connected_residue_at_lower(), core::conformation::Residue::connected_residue_at_upper(), const_residue_(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::conformation::get_second_atom_from_connection(), core::conformation::Residue::has_lower_connect(), core::conformation::Residue::has_upper_connect(), core::conformation::Residue::has_variant_type(), core::chemical::ResidueType::is_aramid(), core::chemical::ResidueType::is_post_methylene_ortho_aramid(), core::chemical::ResidueType::is_pre_methylene_ortho_aramid(), core::chemical::ResidueType::is_pre_methylene_post_methylene_ortho_aramid(), core::chemical::ResidueType::lower_connect_id(), core::chemical::METHYLATED_CTERMINUS_VARIANT, core::chemical::N_ACETYLATION, core::conformation::Residue::residue_connect_atom_index(), core::conformation::Residue::residue_connection_conn_id(), residues_, core::id::AtomID::rsd(), torsion(), core::conformation::Residue::type(), and core::chemical::ResidueType::upper_connect_id().
Referenced by backbone_torsion_angle_atoms().
◆ backbone_torsion_angle_atoms_para_aramid()
|
private |
Get four backbone atoms which define this backbone torsion, if this residue is an aramid.
References core::conformation::Residue::atom_index(), core::id::AtomID::atomno(), core::conformation::Residue::connect_map_size(), core::conformation::Residue::connected_residue_at_lower(), core::conformation::Residue::connected_residue_at_upper(), const_residue_(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::conformation::get_second_atom_from_connection(), core::conformation::Residue::has_lower_connect(), core::conformation::Residue::has_upper_connect(), core::conformation::Residue::has_variant_type(), core::chemical::ResidueType::is_aramid(), core::chemical::ResidueType::is_post_methylene_para_aramid(), core::chemical::ResidueType::is_pre_methylene_para_aramid(), core::chemical::ResidueType::is_pre_methylene_post_methylene_para_aramid(), core::chemical::ResidueType::lower_connect_id(), core::chemical::METHYLATED_CTERMINUS_VARIANT, core::chemical::N_ACETYLATION, core::conformation::Residue::residue_connect_atom_index(), core::conformation::Residue::residue_connection_conn_id(), residues_, core::id::AtomID::rsd(), torsion(), core::conformation::Residue::type(), and core::chemical::ResidueType::upper_connect_id().
Referenced by backbone_torsion_angle_atoms().
◆ batch_get_xyz()
|
virtual |
References xyz().
◆ batch_set_xyz()
|
virtual |
Reimplemented in core::conformation::symmetry::SymmetricConformation.
References atom_tree_, residues_, and set_xyz_moved().
Referenced by apply_transform_Rx_plus_v(), core::conformation::symmetry::SymmetricConformation::apply_transform_Rx_plus_v(), core::conformation::symmetry::SymmetricConformation::batch_set_xyz(), and core::conformation::UltraLightResidue::update_conformation().
◆ begin() [1/2]
|
inlinenoexcept |
References residues_.
◆ begin() [2/2]
|
inlinenoexcept |
References residues_.
Referenced by copy_segment(), and core::conformation::symmetry::MirrorSymmetricConformation::replace_residue().
◆ block_signals()
| void core::conformation::Conformation::block_signals | ( | ) |
block signals from being sent
- Warning
- for safety, ConnectionEvents are never blocked
References general_obs_hub_, identity_obs_hub_, length_obs_hub_, and xyz_obs_hub_.
◆ blocking_signals()
| bool core::conformation::Conformation::blocking_signals | ( | ) | const |
are signals being blocked?
References general_obs_hub_.
◆ bond_angle()
| Real core::conformation::Conformation::bond_angle | ( | AtomID const & | atom1, |
| AtomID const & | atom2, | ||
| AtomID const & | atom3 | ||
| ) | const |
Returns the bond angle defined by <atom[1-3]> through the AtomTree.
References atom_tree_.
Referenced by protocols::simple_moves::RepeatPropagationMover::copy_phi_psi_omega(), protocols::abinitio::abscript::fix_mainchain_connect(), protocols::topology_broker::fix_mainchain_connect(), core::conformation::idealize_position(), core::conformation::insert_ideal_bonds_at_polymer_junction(), core::conformation::insert_ideal_mainchain_bonds(), protocols::backbone_moves::local_backbone_mover::Residue::Residue(), and core::fragment::BBTorsionAndAnglesSRFD::steal().
◆ bond_length()
| Real core::conformation::Conformation::bond_length | ( | AtomID const & | atom1, |
| AtomID const & | atom2 | ||
| ) | const |
Returns the bond length between <atom1> and <atom2> through the AtomTree.
References atom_tree_.
Referenced by protocols::simple_moves::RepeatPropagationMover::copy_phi_psi_omega(), protocols::abinitio::abscript::fix_mainchain_connect(), protocols::topology_broker::fix_mainchain_connect(), core::conformation::idealize_position(), core::conformation::insert_ideal_bonds_at_polymer_junction(), core::conformation::insert_ideal_mainchain_bonds(), and protocols::backbone_moves::local_backbone_mover::Residue::Residue().
◆ bond_orientation() [1/2]
| core::Vector core::conformation::Conformation::bond_orientation | ( | AtomID const & | atom1, |
| AtomID const & | atom2 | ||
| ) | const |
Return the normalized vector of the bond between these two atoms.
This function assumes a bond and will return an orientation even if the atoms are not technically bonded.
References xyz().
Referenced by bond_orientation(), and core::conformation::find_bond_torsion_with_nearest_orientation().
◆ bond_orientation() [2/2]
| core::Vector core::conformation::Conformation::bond_orientation | ( | core::id::TorsionID const | torsion | ) | const |
Return the normalized vector of the bond about which this torsion angle twists.
This function will only work properly if all the reference atoms for <torsion> are defined. If they are not defined, the function will return a zero vector.
References bond_orientation(), get_torsion_angle_atom_ids(), and torsion().
◆ bonded_neighbor_all_res()
| utility::vector1< id::AtomID > core::conformation::Conformation::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.
If intra_res is false, we only find inter - residue neighbors
virtual atoms are excluded by default
References core::conformation::Residue::actual_residue_connection(), core::id::AtomID::atomno(), core::conformation::Residue::bonded_neighbor(), core::conformation::Residue::connection_incomplete(), core::chemical::ResConnID::connid(), core::chemical::ResidueType::is_canonical(), core::chemical::ResidueType::is_solvent(), core::chemical::ResidueType::is_virtual(), core::conformation::Residue::is_virtual(), core::conformation::Residue::n_possible_residue_connections(), core::chemical::ResConnID::resid(), residue(), core::conformation::Residue::residue_connect_atom_index(), core::id::AtomID::rsd(), and core::conformation::Residue::type().
Referenced by protocols::sewing::hashing::AlignmentFileGeneratorMover::add_pose_segments_to_segment_vector(), core::select::residue_selector::BondedResidueSelector::apply(), protocols::branch_angle::branching_atomid1(), protocols::branch_angle::branching_atomids2(), core::scoring::MultipoleElecPotential::determine_polarization_groups(), core::scoring::MultipoleElecPotential::find_params_and_neighbors(), core::io::pose_to_sfr::PoseToStructFileRepConverter::grab_conect_records_for_atom(), is_bonded(), and protocols::simple_moves::ConstrainToIdealMover::vary_bond_geometry().
◆ branch_connection_torsion_angle_atoms()
|
private |
Find the four atoms that define the torsion angle of this branch connection.
This method figures out which four atoms define the torsion angle about the given branch connection point and sets the four AtomIDs passed to it.
- Parameters
-
<torsion> the TorsionID for this branch connection, which must have the BRANCH TorsionType <id1> through <id2>: AtomID variables that will be filled with the found atoms
- Returns
- TRUE to signal FAILURE. (That wasn't my idea! ~Labonte)
- Note
- This method was written to model the behavior of the backbone_torsion_angle_atoms() method and is used like it within the more general get_torsion_angle_atom_ids() method.
References core::id::BRANCH, core::conformation::Residue::connect_atom(), const_residue_(), core::conformation::Residue::first_adjacent_heavy_atom(), core::conformation::Residue::is_branch_point(), core::conformation::Residue::n_non_polymeric_residue_connections(), core::conformation::Residue::n_polymeric_residue_connections(), core::conformation::Residue::residue_connection_partner(), residues_, core::conformation::Residue::seqpos(), torsion(), and core::conformation::TR().
Referenced by get_torsion_angle_atom_ids().
◆ buffer_signals()
| void core::conformation::Conformation::buffer_signals | ( | ) |
block signals from being sent and buffer them to be sent after unblocking
References general_obs_hub_, identity_obs_hub_, length_obs_hub_, and xyz_obs_hub_.
Referenced by protocols::denovo_design::add_residues_to_pose().
◆ buffering_signals()
| bool core::conformation::Conformation::buffering_signals | ( | ) | const |
are signals being blocked and buffered?
References general_obs_hub_.
◆ chain_begin()
Returns the position number of the first residue in chain number <chain>
See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.
References chain_endings_, and num_chains().
Referenced by protocols::splice::Splice::add_sequence_constraints(), protocols::splice::SpliceManager::add_sequence_constraints(), protocols::anchored_design::AnchorMoversData::anchor_noise_constraints_setup(), protocols::dna::SeparateDnaFromNonDna::apply(), protocols::ligand_docking::AddHydrogens::apply(), protocols::ligand_docking::GrowLigand::apply(), protocols::ligand_docking::LigandDesign::apply(), protocols::ligand_docking::MinimizeLigand::apply(), protocols::ligand_docking::ProtLigEnsemble::apply(), protocols::ligand_docking::RandomConformers::apply(), protocols::ligand_docking::TetherLigand::apply(), protocols::ligand_docking::Transform::apply(), protocols::ligand_docking::TransformEnsemble::apply(), protocols::ligand_docking::Translate::apply(), protocols::ligand_docking::WriteLigandMolFile::apply(), protocols::metal_interface::ZincHeterodimerMover::apply(), protocols::ncbb::NcbbDockDesignProtocol::apply(), protocols::ncbb::oop::OopCreatorMover::apply(), protocols::ncbb::oop::OopDockDesignProtocol::apply(), protocols::protein_interface_design::movers::AddSidechainConstraintsToHotspots::apply(), protocols::protein_interface_design::movers::PlacementAuctionMover::apply(), protocols::protein_interface_design::movers::PlaceStubMover::apply(), protocols::protein_interface_design::movers::SetAtomTree::apply(), protocols::seeded_abinitio::CAcstGenerator::apply(), protocols::seeded_abinitio::CloseFold::apply(), protocols::seeded_abinitio::DefineMovableLoops::apply(), protocols::seeded_abinitio::SegmentHybridizer::apply(), protocols::seeded_abinitio::SwapSegment::apply(), protocols::simple_moves::AlignChainMover::apply(), protocols::simple_moves::CyclizationMover::apply(), protocols::simple_moves::DeleteChainsMover::apply(), protocols::simple_moves::DisulfideInsertionMover::apply(), protocols::simple_moves::FavorSequenceProfile::apply(), protocols::simple_moves::ReportXYZ::apply(), protocols::simple_moves::SetTorsion::apply(), protocols::simple_moves::SwitchChainOrderMover::apply(), protocols::task_operations::PreventChainFromRepackingOperation::apply(), protocols::task_operations::RestrictChainToRepackingOperation::apply(), protocols::task_operations::RestrictToAlignedSegmentsOperation::apply(), protocols::task_operations::RestrictToTerminiOperation::apply(), protocols::task_operations::SelectResiduesWithinChainOperation::apply(), protocols::task_operations::ThreadSequenceOperation::apply(), protocols::ligand_docking::AtomCountFilter::apply(), protocols::ligand_docking::CompleteConnectionsFilter::apply(), protocols::ligand_docking::HBondAcceptorFilter::apply(), protocols::ligand_docking::HBondDonorFilter::apply(), protocols::ligand_docking::MolarMassFilter::apply(), protocols::ligand_docking::MolecularMassFilter::apply(), protocols::simple_moves::AddJobPairData::apply(), protocols::fldsgn::CircularPermutation::apply(), protocols::matdes::SymDofMover::apply(), protocols::protein_interface_design::movers::BackrubDDMover::apply(), protocols::protein_interface_design::movers::PlaceOnLoop::apply(), protocols::protein_interface_design::movers::TopologyBrokerMover::apply(), protocols::task_operations::JointSequenceOperation::apply(), protocols::task_operations::SeqprofConsensusOperation::apply(), protocols::protein_interface_design::best_bbcst_residues(), protocols::denovo_design::components::calc_paired_residues(), protocols::anchored_design::AnchoredDesignMover::calculate_rmsd(), protocols::simple_moves::CutChainMover::chain_cut(), protocols::splice::Splice::chainbreak_check(), protocols::splice::SpliceManager::chainbreak_check(), protocols::protein_interface_design::filters::AtomicContactCountFilter::compute(), protocols::protein_interface_design::filters::AverageDegreeFilter::compute(), protocols::protein_interface_design::filters::HbondsToAtomFilter::compute(), protocols::simple_filters::AngleToVector::compute(), protocols::simple_filters::ChainBreak::compute(), protocols::simple_filters::NeighborTypeFilter::compute(), protocols::simple_filters::ResidueBurialFilter::compute(), protocols::simple_filters::TerminusDistanceFilter::compute(), protocols::ligand_docking::Transform::convert_to_full_pose(), protocols::ligand_docking::TransformEnsemble::convert_to_full_pose(), protocols::protein_interface_design::movers::SetAtomTree::create_atom_tree(), protocols::floppy_tail::create_extra_output(), protocols::simple_moves::CutChainMover::create_subpose(), protocols::seeded_abinitio::define_movemap_chains(), protocols::peptide_deriver::PeptideDeriverFilter::derive_peptide(), core::pack::hbonds::determine_atom_level_edge_info(), protocols::simple_moves::DisulfideInsertionMover::determine_cyclization_viability(), protocols::protein_interface_design::movers::PlaceStubMover::disallowed_host_pos(), protocols::ligand_docking::InterfaceBuilder::enforce_minimum_length(), core::pose::metrics::simple_calculators::InterfaceDefinitionCalculator::fill_in_chain_terminii(), protocols::ligand_docking::InterfaceBuilder::find_interface_residues(), protocols::protein_interface_design::find_lowest_constraint_energy_residue(), protocols::protein_interface_design::find_nearest_residue(), protocols::protein_interface_design::movers::find_nearest_residue_to_coord(), core::select::util::find_neighbors_within_CB_cutoff(), core::pack::hbonds::HBondGraphInitializerIG::find_symmetric_hbonds(), protocols::splice::Splice::fold_tree(), protocols::forge::methods::fold_tree_from_loops(), protocols::forge::methods::fold_tree_from_pose(), protocols::pose_creation::MakeJunctionsMover::generate_start_pose(), protocols::protein_interface_design::movers::MapHotspot::GenerateMap(), core::conformation::symmetry::get_chain2range(), core::pose::get_chain_from_chain_id(), core::pose::get_chain_residues(), protocols::antibody::AntibodyInfo::get_FoldTree_LH_A(), protocols::hotspot_hashing::HotspotStub::get_nearest_residue(), core::scoring::methods::NMerSVMEnergy::get_residue_energy_by_svm(), core::pose::get_resnums_for_chain_id(), protocols::floppy_tail::FloppyTailMover::init_on_new_input(), protocols::ligand_docking::ComputeLigandRDF::ligand_protein_rdf(), protocols::loops::loopfinder(), protocols::loops::loops_around_residues(), protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover::make_disjointed_foldtree(), protocols::protein_interface_design::make_hotspot_foldtree(), protocols::denovo_design::components::make_lengths_str(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::minimize_all(), protocols::protein_interface_design::MinimizeInterface(), protocols::protein_interface_design::movers::MapHotspot::output_pose(), protocols::chemically_conjugated_docking::pack_extra_bodies(), protocols::protein_interface_design::movers::PlaceStubMover::place_stub(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::place_stubs(), protocols::denovo_design::components::pose_matches_description(), protocols::hotspot_hashing::HotspotStubSet::prepare_hashing_packer_task_(), protocols::peptide_deriver::PeptideDeriverFilter::prepare_pose(), protocols::ligand_docking::ProtLigEnsemble::prepare_single_ligand_pose(), protocols::cyclic_peptide::PeptideStubMover::preserve_old_mainchain_torsions(), protocols::ligand_docking::ComputeLigandRDF::protein_protein_rdf(), protocols::denovo_design::components::prune_unpaired_residues(), protocols::peptide_deriver::PeptideDeriverFilter::push_chain_residue_indices(), core::io::pose_to_sfr::PoseToStructFileRepConverter::recalculate_new_chainIDs(), protocols::splice::AlignEndsMover::reference_positions(), protocols::protein_interface_design::movers::PlacementMinimizationMover::refresh_bbstub_constraints(), protocols::analysis::InterfaceAnalyzerMover::reorder_foldtree_find_jump(), protocols::forge::remodel::RemodelLoopMover::repeat_generation_with_additional_residue(), protocols::forge::remodel::RemodelLoopMover::repeat_propagation(), protocols::features::ScreeningFeatures::report_features(), protocols::ligand_docking::HeavyAtomFilter::report_sm(), core::scoring::membrane::MPNonHelixPenalty::residue_energy(), core::scoring::methods::NMerPSSMEnergy::residue_energy(), protocols::simple_filters::NonSequentialNeighborsFilter::residue_neighbors(), core::pose::ResidueIndexDescriptionChainEnd::resolve_index(), protocols::ligand_docking::Rotate::rotate_ligand(), core::select::residue_selector::ChainSelector::select_chain_by_index(), protocols::protein_interface_design::movers::SetAtomTree::set_ab_fold_tree(), protocols::ligand_docking::MoveMapBuilder::set_all_chi(), protocols::splice::SpliceOut::set_fold_tree_nodes(), protocols::splice::SpliceIn::set_fold_tree_nodes(), protocols::splice::SpliceInAntibody::set_fold_tree_nodes(), protocols::splice::SpliceInTail::set_fold_tree_nodes(), protocols::splice::SpliceOutAntibody::set_fold_tree_nodes(), protocols::splice::SpliceOutTail::set_fold_tree_nodes(), protocols::seeded_abinitio::SeedSetupMover::set_packerTasks_target_and_seeds(), protocols::hbnet::HBNet::set_symmetry(), protocols::qsar::scoring_grid::ChargeGrid::setup_charge_atoms(), core::scoring::constraints::FabConstraint::setup_csts(), core::scoring::constraints::SiteConstraint::setup_csts(), core::energy_methods::Abego::setup_for_scoring(), protocols::antibody::AntibodyInfo::setup_FrameWorkInfo(), protocols::simple_moves::CyclizationMover::setup_minimizer(), protocols::ncbb::setup_pert_foldtree(), protocols::relax::membrane::MPFastRelaxMover::setup_relax_foldtree(), core::conformation::symmetry::setup_symmetric_conformation(), protocols::fldsgn::CircularPermutation::split_chains(), protocols::protein_interface_design::star_fold_tree(), protocols::protein_interface_design::movers::PlaceStubMover::StubMinimize(), protocols::seeded_abinitio::SwapSegment::swap_chain(), protocols::ligand_docking::Rotate_info::tag_along_residues(), protocols::splice::Splice::tail_fold_tree(), protocols::protein_interface_design::PatchdockReader::transform_pose(), and protocols::fldsgn::CircularPermutation::which_chain().
◆ chain_end()
Returns the position number of the last residue in chain number <chain>
See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.
References chain_endings_, and size().
Referenced by protocols::splice::SpliceOutTail::abstract_parse_tag(), protocols::splice::Splice::add_sequence_constraints(), protocols::splice::SpliceManager::add_sequence_constraints(), protocols::splice::SpliceManager::adjust_stem_positions_by_template(), protocols::chemically_conjugated_docking::UBQ_GTPaseMover::analyze_and_filter(), protocols::anchored_design::AnchorMoversData::anchor_noise_constraints_setup(), protocols::ligand_docking::AddHydrogens::apply(), protocols::ligand_docking::GrowLigand::apply(), protocols::ligand_docking::LigandDesign::apply(), protocols::ligand_docking::MinimizeLigand::apply(), protocols::ligand_docking::RandomConformers::apply(), protocols::metal_interface::ZincHeterodimerMover::apply(), protocols::ncbb::oop::OopCreatorMover::apply(), protocols::protein_interface_design::movers::AddSidechainConstraintsToHotspots::apply(), protocols::protein_interface_design::movers::PlacementAuctionMover::apply(), protocols::protein_interface_design::movers::PlaceStubMover::apply(), protocols::protein_interface_design::movers::SetAtomTree::apply(), protocols::seeded_abinitio::CAcstGenerator::apply(), protocols::seeded_abinitio::CloseFold::apply(), protocols::seeded_abinitio::DefineMovableLoops::apply(), protocols::simple_moves::AlignChainMover::apply(), protocols::simple_moves::CyclizationMover::apply(), protocols::simple_moves::DeleteChainsMover::apply(), protocols::simple_moves::DisulfideInsertionMover::apply(), protocols::simple_moves::ReportXYZ::apply(), protocols::simple_moves::SetTorsion::apply(), protocols::simple_moves::SwitchChainOrderMover::apply(), protocols::task_operations::PreventChainFromRepackingOperation::apply(), protocols::task_operations::ProteinInterfaceDesignOperation::apply(), protocols::task_operations::RestrictChainToRepackingOperation::apply(), protocols::task_operations::RestrictToTerminiOperation::apply(), protocols::task_operations::ThreadSequenceOperation::apply(), protocols::ligand_docking::AtomCountFilter::apply(), protocols::ligand_docking::CompleteConnectionsFilter::apply(), protocols::ligand_docking::HBondAcceptorFilter::apply(), protocols::ligand_docking::HBondDonorFilter::apply(), protocols::ligand_docking::MolarMassFilter::apply(), protocols::ligand_docking::MolecularMassFilter::apply(), protocols::fldsgn::CircularPermutation::apply(), protocols::matdes::SymDofMover::apply(), protocols::protein_interface_design::movers::BackrubDDMover::apply(), protocols::protein_interface_design::movers::PlaceOnLoop::apply(), protocols::protein_interface_design::movers::TopologyBrokerMover::apply(), protocols::simple_moves::FoldTreeFromMotif::apply(), protocols::splice::Splice::apply(), protocols::task_operations::JointSequenceOperation::apply(), protocols::task_operations::SeqprofConsensusOperation::apply(), protocols::splice::SpliceOutAntibody::assign_from_res_to_res(), protocols::splice::SpliceInAntibody::assign_from_res_to_res(), protocols::splice::SpliceInTail::assign_from_res_to_res(), protocols::protein_interface_design::best_bbcst_residues(), protocols::denovo_design::components::calc_paired_residues(), protocols::anchored_design::AnchoredDesignMover::calculate_rmsd(), protocols::simple_moves::CutChainMover::chain_cut(), core::pose::chain_end_res(), protocols::splice::Splice::chainbreak_check(), protocols::splice::SpliceManager::chainbreak_check(), protocols::splice::SampleRotamersFromPDB::combine_rot_dbs(), protocols::protein_interface_design::filters::AtomicContactCountFilter::compute(), protocols::protein_interface_design::filters::AverageDegreeFilter::compute(), protocols::protein_interface_design::filters::ClashWithTargetFilter::compute(), protocols::simple_filters::ChainBreak::compute(), protocols::simple_filters::ResidueBurialFilter::compute(), protocols::simple_filters::TerminusDistanceFilter::compute(), protocols::ligand_docking::Transform::convert_to_full_pose(), protocols::ligand_docking::TransformEnsemble::convert_to_full_pose(), protocols::splice::Splice::copy_stretch(), protocols::protein_interface_design::movers::SetAtomTree::create_atom_tree(), protocols::ligand_docking::Rotate::create_random_rotations(), protocols::simple_moves::CutChainMover::create_subpose(), protocols::seeded_abinitio::define_movemap_chains(), protocols::peptide_deriver::PeptideDeriverFilter::derive_peptide(), core::pack::hbonds::determine_atom_level_edge_info(), protocols::protein_interface_design::movers::PlaceStubMover::disallowed_host_pos(), protocols::ligand_docking::InterfaceBuilder::enforce_minimum_length(), protocols::indexed_structure_store::extract_residue_entries(), core::pose::metrics::simple_calculators::InterfaceDefinitionCalculator::fill_in_chain_terminii(), protocols::ligand_docking::InterfaceBuilder::find_interface_residues(), protocols::protein_interface_design::find_lowest_constraint_energy_residue(), protocols::protein_interface_design::find_nearest_residue(), protocols::protein_interface_design::movers::find_nearest_residue_to_coord(), core::select::util::find_neighbors_within_CB_cutoff(), core::pack::hbonds::HBondGraphInitializerIG::find_symmetric_hbonds(), protocols::splice::Splice::fold_tree(), protocols::forge::methods::fold_tree_from_loops(), protocols::forge::methods::fold_tree_from_pose(), protocols::simple_moves::CutChainMover::foldTree(), protocols::pose_creation::MakeJunctionsMover::generate_start_pose(), core::conformation::symmetry::get_chain2range(), core::pose::get_chain_residues(), core::pack::dunbrack::PeptoidOmegaReporter::get_dof(), protocols::antibody::AntibodyInfo::get_FoldTree_AllCDRs_LHDock(), protocols::antibody::AntibodyInfo::get_FoldTree_L_HA(), protocols::antibody::AntibodyInfo::get_FoldTree_LA_H(), protocols::antibody::AntibodyInfo::get_FoldTree_LH_A(), protocols::indexed_structure_store::FragmentLookup::get_fragment_residue_spans(), protocols::hotspot_hashing::HotspotStub::get_nearest_residue(), core::scoring::methods::NMerSVMEnergy::get_residue_energy_by_svm(), core::scoring::methods::NMerRefEnergy::get_residue_energy_by_table(), core::pose::get_resnums_for_chain_id(), protocols::floppy_tail::FloppyTailMover::init_on_new_input(), protocols::chemically_conjugated_docking::UBQ_GTPaseMover::initialize(), core::pack::dunbrack::PeptoidOmegaReporter::insert_atoms_defining_dof(), insert_conformation_by_jump(), protocols::ligand_docking::ComputeLigandRDF::ligand_protein_rdf(), protocols::loops::loopfinder(), protocols::loops::loops_around_residues(), protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover::make_disjointed_foldtree(), protocols::protein_interface_design::make_hotspot_foldtree(), protocols::denovo_design::components::make_lengths_str(), protocols::splice::min_seg(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::minimize_all(), protocols::protein_interface_design::MinimizeInterface(), protocols::splice::nearest_to_entry_stop_on_pose(), core::conformation::Residue::orient_onto_residue_peptoid(), protocols::chemically_conjugated_docking::pack_extra_bodies(), protocols::protein_interface_design::movers::PlaceStubMover::place_stub(), protocols::protein_interface_design::movers::PlaceSimultaneouslyMover::place_stubs(), protocols::denovo_design::components::pose_matches_description(), protocols::hotspot_hashing::HotspotStubSet::prepare_hashing_packer_task_(), protocols::peptide_deriver::PeptideDeriverFilter::prepare_pose(), protocols::cyclic_peptide::PeptideStubMover::preserve_old_mainchain_torsions(), protocols::ligand_docking::ComputeLigandRDF::protein_protein_rdf(), protocols::denovo_design::components::prune_unpaired_residues(), protocols::peptide_deriver::PeptideDeriverFilter::push_chain_residue_indices(), core::io::pose_to_sfr::PoseToStructFileRepConverter::recalculate_new_chainIDs(), protocols::splice::AlignEndsMover::reference_positions(), protocols::protein_interface_design::movers::PlacementMinimizationMover::refresh_bbstub_constraints(), protocols::splice::Splice::remove_hairpin(), protocols::splice::SpliceOut::remove_hairpin(), protocols::analysis::InterfaceAnalyzerMover::reorder_foldtree_find_jump(), protocols::forge::remodel::RemodelLoopMover::repeat_generation_with_additional_residue(), protocols::forge::remodel::RemodelLoopMover::repeat_propagation(), protocols::features::ScreeningFeatures::report_features(), protocols::ligand_docking::HeavyAtomFilter::report_sm(), core::scoring::methods::NMerPSSMEnergy::residue_energy(), protocols::simple_filters::NonSequentialNeighborsFilter::residue_neighbors(), core::pose::ResidueIndexDescriptionChainEnd::resolve_index(), core::select::residue_selector::ChainSelector::select_chain_by_index(), protocols::protein_interface_design::movers::SetAtomTree::set_ab_fold_tree(), protocols::ligand_docking::MoveMapBuilder::set_all_chi(), protocols::anchored_design::AnchoredDesignMover::set_fold_tree_and_cutpoints(), protocols::splice::SpliceOut::set_fold_tree_nodes(), protocols::splice::SpliceIn::set_fold_tree_nodes(), protocols::splice::SpliceInAntibody::set_fold_tree_nodes(), protocols::splice::SpliceInTail::set_fold_tree_nodes(), protocols::splice::SpliceOutAntibody::set_fold_tree_nodes(), protocols::splice::SpliceOutTail::set_fold_tree_nodes(), protocols::splice::RBInMover::set_fold_tree_nodes(), protocols::splice::RBOutMover::set_fold_tree_nodes(), protocols::splice::SpliceOutTail::set_source_from_to_res(), protocols::hbnet::HBNet::set_symmetry(), protocols::qsar::scoring_grid::ChargeGrid::setup_charge_atoms(), core::scoring::constraints::FabConstraint::setup_csts(), core::scoring::constraints::SiteConstraint::setup_csts(), protocols::docking::setup_foldtree(), core::energy_methods::Abego::setup_for_scoring(), protocols::antibody::AntibodyInfo::setup_FrameWorkInfo(), protocols::simple_moves::CyclizationMover::setup_minimizer(), protocols::ncbb::setup_pert_foldtree(), protocols::relax::membrane::MPFastRelaxMover::setup_relax_foldtree(), core::conformation::symmetry::setup_symmetric_conformation(), protocols::fldsgn::CircularPermutation::split_chains(), protocols::protein_interface_design::star_fold_tree(), protocols::protein_interface_design::movers::PlaceStubMover::StubMinimize(), protocols::seeded_abinitio::SwapSegment::swap_chain(), protocols::ligand_docking::Rotate_info::tag_along_residues(), protocols::splice::Splice::tail_fold_tree(), protocols::protein_interface_design::PatchdockReader::transform_pose(), and protocols::fldsgn::CircularPermutation::which_chain().
◆ chain_endings() [1/2]
| utility::vector1< Size > const & core::conformation::Conformation::chain_endings | ( | ) | const |
Returns the list of (chain number) chain endings.
See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.
References chain_endings_.
Referenced by protocols::grafting::simple_movers::DeleteRegionMover::apply(), protocols::protein_interface_design::movers::AddChainBreak::apply(), protocols::indexed_structure_store::apply_residue_entries_to_pose(), core::pose::chain_end_res(), protocols::denovo_design::components::StructureData::check_chains(), protocols::denovo_design::components::compute_chain_beginnings(), protocols::denovo_design::components::RemodelLoopMoverPoseFolder::create_remodel_loop_mover(), core::io::silent::BinarySilentStruct::fill_pose(), core::io::silent::ProteinSilentStruct_Template< T >::fill_pose(), core::io::silent::BinarySilentStruct::fill_struct(), core::io::silent::ProteinSilentStruct_Template< T >::fill_struct(), protocols::seeded_abinitio::CloseFold::find_loops(), protocols::seeded_abinitio::DefineMovableLoops::find_loops(), protocols::denovo_design::components::Picker::fragments_for_permutation_take_X_from_pose(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_residue_information(), protocols::denovo_design::components::StructureDataFactory::infer_from_pose(), protocols::features::PoseConformationFeatures::load_chain_endings(), protocols::forge::build::SegmentRebuild::modify_impl(), protocols::chemically_conjugated_docking::pack_extra_bodies(), protocols::legacy_sewing::LegacyAppendAssemblyMover::refine_assembly(), core::pose::renumber_pdbinfo_based_on_conf_chains(), protocols::features::LoopAnchorFeatures::report_features(), protocols::features::PoseConformationFeatures::report_features_implementation(), protocols::glycopeptide_docking::GlycopeptideDockingFlags::set_enzyme_chain(), protocols::glycopeptide_docking::GlycopeptideDockingFlags::set_substrate_chain(), protocols::legacy_sewing::Assembly::to_multichain_pose(), and protocols::surface_docking::SurfaceDockingProtocol::valid_surface_pose().
◆ chain_endings() [2/2]
|
virtual |
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 in protocols::environment::ProtectedConformation.
References chain_endings_, rederive_chain_ids(), and size().
◆ chains_from_termini()
|
virtual |
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 in protocols::environment::ProtectedConformation.
References chain_endings_, rederive_chain_ids(), residues_, and size().
Referenced by protocols::loop_grower::LoopGrower::addnativesolution(), protocols::grafting::simple_movers::DeleteRegionMover::apply(), protocols::loop_grower::LoopGrower::apply(), protocols::hybridization::HybridizeProtocol::apply(), protocols::loop_grower::LoopPartialSolutionStore::cluster_check(), protocols::denovo_design::components::ExtendedPoseBuilder::extend_pose(), protocols::loop_grower::LoopPartialSolutionStore::filter(), protocols::forge::build::BuildManager::modify(), protocols::denovo_design::movers::new_jump_and_cutpoint(), protocols::loop_grower::LoopPartialSolutionStore::push(), protocols::loop_grower::LoopGrower::refine_cycle(), protocols::loop_grower::LoopGrower::rescoresolutionset(), and protocols::loop_grower::LoopGrower::update_to_stored().
◆ check_valid_membrane()
| void core::conformation::Conformation::check_valid_membrane | ( | ) | const |
Check that a new membrane position is valid.
Given a new membrane normal/center pair, check that the newly constructed stub represents an orthogonal coordinate frame
References downstream_jump_stub(), core::kinematics::Stub::is_orthogonal(), jump(), and membrane_info_.
Referenced by update_membrane_position().
◆ clear()
| void core::conformation::Conformation::clear | ( | ) |
clear data
References atom_tree_, chain_endings_, core::chemical::CacheableResidueTypeSets::clear(), core::id::AtomID_Map< T >::clear(), clear_glycan_trees(), dof_moved_, fold_tree_, parameters_set_, pre_nresidue_change(), residue_type_sets_, residues_, and xyz_moved_.
Referenced by operator=(), protocols::stepwise::modeler::slice(), protocols::pose_length_moves::NearNativeLoopCloser::switch_chain_order(), core::conformation::symmetry::MirrorSymmetricConformation::~MirrorSymmetricConformation(), and core::conformation::symmetry::SymmetricConformation::~SymmetricConformation().
◆ clear_glycan_trees()
| void core::conformation::Conformation::clear_glycan_trees | ( | ) |
Safely detaches any tree observers and clears it to null.
References tree_set_observer_.
Referenced by clear(), core::pose::symmetry::extract_asymmetric_unit(), core::pose::symmetry::get_asymmetric_pose_copy_from_symmetric_pose(), insert_conformation_by_jump(), core::pose::symmetry::make_asymmetric_pose(), and core::pose::symmetry::make_symmetric_pose().
◆ clear_observers()
| void core::conformation::Conformation::clear_observers | ( | ) |
clear all observers
- Remarks
- ConnectionEvent::DISCONNECT will be sent to all observers
References connection_obs_hub_, core::conformation::signals::ConnectionEvent::DISCONNECT, general_obs_hub_, identity_obs_hub_, length_obs_hub_, notify_connection_obs(), and xyz_obs_hub_.
◆ clear_parameters_set_list()
| void core::conformation::Conformation::clear_parameters_set_list | ( | ) |
Delete the list of ParametersSetOP objects.
References parameters_set_.
Referenced by protocols::helical_bundle::MakeBundle::apply(), protocols::pose_length_moves::FixAllLoopsMover::apply(), protocols::pose_length_moves::NearNativeLoopCloser::apply(), and protocols::pose_length_moves::ConnectChainsMover::reletter_chains().
◆ clone()
|
virtual |
clone the conformation
make a copy of this conformation( allocate actual memory for it )
Reimplemented in protocols::environment::ProtectedConformation, core::conformation::symmetry::SymmetricConformation, and core::conformation::symmetry::MirrorSymmetricConformation.
Referenced by protocols::stepwise::modeler::rna::sugar::VirtualSugarSamplerFromStringList::apply(), core::conformation::symmetry::MirrorSymmetricConformation::insert_conformation_by_jump(), core::conformation::symmetry::SymmetricConformation::insert_conformation_by_jump(), and core::conformation::symmetry::setup_symmetric_conformation().
◆ const_residue_()
|
inlineprotected |
Returns a constant residue reference without triggering coordinate/torsion update.
Use with care. Useful inside torsion/coordinate setters where we want chemical info about a given residue but don't want to trigger the coordinate/torsion updates that go along with a call to residue(seqpos).
References residues_, and size().
Referenced by atom_tree_torsion(), atoms_are_bonded(), backbone_torsion_angle_atoms(), backbone_torsion_angle_atoms_meta_aramid(), backbone_torsion_angle_atoms_oligourea(), backbone_torsion_angle_atoms_ortho_aramid(), backbone_torsion_angle_atoms_para_aramid(), branch_connection_torsion_angle_atoms(), get_torsion_angle_atom_ids(), jump_atom_id(), core::conformation::symmetry::SymmetricConformation::prepend_polymer_residue_before_seqpos(), and resolve_partial_atom_id().
◆ const_residues()
| ResidueCOPs core::conformation::Conformation::const_residues | ( | ) | const |
Inefficient – constructs copy of residues_.
References residues_, and size().
Referenced by append_residue(), insert_polymer_residue(), insert_residue_by_bond(), insert_residue_by_jump(), replace_residue(), and setup_atom_tree().
◆ contains_carbohydrate_residues() [1/2]
|
inline |
Return true if this conformation contains any carbohydrate residues.
References contains_carbohydrate_residues_.
Referenced by core::import_pose::build_pose_as_is2(), core::scoring::electron_density::calculate_rama(), core::pose::carbohydrates::delete_carbohydrate_branch(), core::pose::symmetry::extract_asymmetric_unit(), core::pose::symmetry::get_asymmetric_pose_copy_from_symmetric_pose(), core::pose::carbohydrates::glycosylate_pose(), insert_conformation_by_jump(), core::pose::symmetry::make_asymmetric_pose(), core::pose::make_pose_from_saccharide_sequence(), core::pose::symmetry::make_symmetric_pose(), core::io::pose_from_sfr::PoseFromSFRBuilder::refine_pose(), protocols::carbohydrates::TautomerizeAnomerMover::setup_movable_reducing_ends(), and protocols::carbohydrates::RingPlaneFlipMover::setup_movable_torsion_pairs().
◆ contains_carbohydrate_residues() [2/2]
|
inline |
Set whether this conformation contains any carbohydrate residues.
References contains_carbohydrate_residues_.
◆ copy_segment()
| void core::conformation::Conformation::copy_segment | ( | Size | size, |
| Conformation const & | src, | ||
| Size | begin, | ||
| Size | src_begin | ||
| ) |
copy a stretch of coordinates/torsions from another Conformation
copy a stretch of coordinates/torsions from another pose Fires IdentityEvent signals as residues are replaced.
References begin(), replace_residue(), residue(), and size().
◆ create_new_parameters_set()
| void core::conformation::Conformation::create_new_parameters_set | ( | ) |
Create a new (empty) ParametersSet object and add its owning pointer to the current Conformation object.
References parameters_set_.
◆ debug_pause() [1/2]
| bool core::conformation::Conformation::debug_pause | ( | ) | const |
waiting for stdin after sending a GeneralEvent signal?
References general_obs_hub_.
◆ debug_pause() [2/2]
| void core::conformation::Conformation::debug_pause | ( | bool | flag | ) | const |
wait for stdin after sending a GeneralEvent signal
References general_obs_hub_.
◆ debug_residue_torsions()
| void core::conformation::Conformation::debug_residue_torsions | ( | bool | verbose = false | ) | const |
debugging
check that the residue torsions are in sync with the residue coords and atomtree coords
References protocols::comparative_modeling::features::A, core::conformation::Residue::atom(), atom_tree_, atom_tree_torsion(), core::id::AtomID::atomno(), core::id::BB, core::conformation::Residue::chi(), core::id::CHI, core::chemical::element::F, fold_tree_, get_torsion_angle_atom_ids(), core::conformation::Residue::mainchain_atoms(), core::conformation::Residue::mainchain_torsion(), core::conformation::Residue::nchi(), core::io::raw_data::precision(), residue(), core::id::AtomID::rsd(), size(), torsion(), update_residue_coordinates(), update_residue_torsions(), and core::conformation::Atom::xyz().
◆ declare_chemical_bond()
|
virtual |
Declare that a chemical bond exists between two residues.
Reimplemented in core::conformation::symmetry::SymmetricConformation, and protocols::environment::ProtectedConformation.
References core::conformation::Residue::atom_index(), core::chemical::ResidueConnection::atomno(), core::conformation::Residue::n_possible_residue_connections(), core::conformation::Residue::name(), residue(), core::conformation::Residue::residue_connection(), core::conformation::Residue::residue_connection_partner(), residue_torsions_need_updating_, residues_, core::conformation::update_cutpoint_virtual_atoms_if_connected(), and update_residue_torsions().
Referenced by core::util::add_covalent_linkage(), protocols::forge::methods::add_cutpoint_variants(), protocols::denovo_design::add_cutpoints(), add_disulfide_bond(), protocols::loops::add_single_cutpoint_variant(), protocols::indel::IndelOptimizationMover::apply(), protocols::loop_grower::LoopGrower::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), protocols::simple_moves::a3b_hbs::A3BHbsPatcher::apply(), protocols::simple_moves::DeclareBond::apply(), protocols::LoopRebuild::build_loop_with_ccd_closure(), core::pose::correctly_add_2prime_connection_variants(), protocols::relax::cyclize_pose(), core::conformation::symmetry::SymmetricConformation::declare_chemical_bond(), core::pose::declare_cutpoint_chemical_bond(), core::io::silent::BinarySilentStruct::fill_pose(), core::pose::fix_up_residue_type_variants_at_strand_beginning(), core::pose::fix_up_residue_type_variants_at_strand_end(), core::conformation::form_disulfide(), protocols::protein_interface_design::movers::DisulfideMover::form_disulfide(), protocols::grafting::insert_pose_into_pose(), protocols::toolbox::match_enzdes_util::EnzConstraintParameters::make_constraint_covalent(), protocols::forge::methods::make_star_foldtree(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_CCD::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD_Moves::model_loop(), protocols::denovo_design::movers::new_jump_and_cutpoint(), core::io::pose_from_sfr::PoseFromSFRBuilder::refine_pose(), protocols::loops::set_loop_cutpoint_in_pose_fold_tree(), protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_chainbreak_variants(), protocols::loop_grower::LoopGrower::single_grow(), and protocols::loop_grower::LoopGrower::update_to_stored().
◆ delete_chain_ending()
|
virtual |
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 in protocols::environment::ProtectedConformation.
References chain_endings_, and rederive_chain_ids().
Referenced by protocols::forge::build::SegmentRebuild::modify_impl().
◆ delete_polymer_residue()
|
virtual |
Delete polymer residue at the given sequence position.
delete a polymer residues Fires a LengthEvent::RESIDUE_DELETE signal.
Reimplemented in protocols::environment::ProtectedConformation.
References atom_tree_, fold_tree_, notify_length_obs(), pre_nresidue_change(), core::conformation::signals::LengthEvent::RESIDUE_DELETE, residue_torsions_need_updating_, residues_delete(), and size().
Referenced by protocols::protein_interface_design::movers::LoopLengthChange::apply().
◆ delete_residue_range_slow()
|
virtual |
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 in protocols::environment::ProtectedConformation.
References atom_tree_, fold_tree_, notify_length_obs(), pre_nresidue_change(), core::conformation::signals::LengthEvent::RESIDUE_DELETE, residue_torsions_need_updating_, residues_delete(), setup_atom_tree(), and size().
Referenced by protocols::cutoutdomain::CutOutDomain::apply(), protocols::indel::IndelOptimizationMover::apply(), protocols::loop_grower::SheetSampler::apply(), protocols::moves::StructureRestrictor::apply(), protocols::simple_moves::DeleteChainsMover::apply(), protocols::antibody_legacy::GraftOneMover::apply(), protocols::fldsgn::CircularPermutation::apply(), protocols::protein_interface_design::movers::TopologyBrokerMover::apply(), protocols::protein_interface_design::filters::AtomicContactCountFilter::compute(), protocols::floppy_tail::create_extra_output(), protocols::stepwise::legacy::modeler::rna::SlicedPoseWorkingParameters::create_sliced_pose(), protocols::pose_creation::MakeJunctionsMover::generate_start_pose(), protocols::hotspot_hashing::HotspotStubSet::get_residue_score_(), protocols::loop_grower::LoopGrower::modifiedscore(), protocols::forge::build::SegmentInsert::modify_impl(), protocols::forge::build::SegmentRebuild::modify_impl(), protocols::forge::build::SegmentSwap::modify_impl(), protocols::environment::Environment::remove_nonpermenant_features(), protocols::hybridization::HybridizeFoldtreeDynamic::reset(), protocols::loop_grower::LoopGrower::sheetscore(), protocols::simple_moves::RepeatPropagationMover::trim_back_repeat_to_repair_scar(), and protocols::pose_creation::MakeJunctionsMover::trim_pose().
◆ delete_residue_slow()
|
virtual |
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 pbradley@fhcrc.org)
LOGIC: uses fold_tree.delete_seqpos to handle shifting the topology around if necessary, then calls setup_atom_tree
Reimplemented in protocols::environment::ProtectedConformation.
References atom_tree_, fold_tree_, notify_length_obs(), pre_nresidue_change(), core::conformation::signals::LengthEvent::RESIDUE_DELETE, residue_torsions_need_updating_, residues_delete(), setup_atom_tree(), size(), unblock_signals(), and xyz_obs_hub_.
Referenced by protocols::cryst::UpdateCrystInfo::apply(), protocols::enzdes::RepackLigandSiteWithoutLigandMover::apply(), protocols::comparative_modeling::PartialThreadingMover::apply(), protocols::forge::components::VarLengthBuild::apply(), protocols::forge::remodel::RemodelMover::apply(), protocols::simple_moves::PeriodicBoxMover::apply(), protocols::simple_moves::VirtualRootMover::apply(), protocols::task_operations::RestrictNativeResiduesOperation::apply(), protocols::loops::apply_sequence_mapping(), protocols::sic_dock::auto_trim_floppy_termini(), protocols::simple_ddg::ddG::clean_pose(), protocols::protein_interface_design::filters::SequenceRecoveryFilter::compute(), protocols::simple_filters::MutationsFilter::compute(), protocols::grafting::delete_overhang_residues(), protocols::relax::delete_virtual_residues(), protocols::simple_moves::ExplicitWaterMover::delete_waters(), protocols::chemically_conjugated_docking::UBQ_GTPaseMover::initialize(), protocols::features::ReportToDB::initialize_pose(), protocols::ligand_docking::HighResEnsemble::prepare_single_ligand_pose(), protocols::match::MatcherMover::process_pose(), core::pose::remove_ligand_canonical_residues(), protocols::toolbox::pose_manipulation::remove_non_protein_residues(), core::pose::remove_nonprotein_residues(), protocols::hybridization::remove_residues(), core::pose::remove_virtual_residues(), protocols::forge::remodel::RemodelLoopMover::repeat_generation_with_additional_residue(), protocols::relax::RepeatProteinRelax::seal_jumps(), protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::setup_native_pose(), protocols::nonlocal::StarTreeBuilder::tear_down(), protocols::star::StarAbinitio::tear_down_kinematics(), protocols::legacy_sewing::Model::trim_db_pose(), and protocols::features::ModelFeatures::trim_pose().
◆ detach_connection_obs()
|
inline |
detach ConnectionEvent observer function
- Parameters
-
fn pointer to observer's unary member function with signature void( ConnectionEvent const & ) ptr RAW pointer to observer object
- Returns
- true if disconnect successful, false if connection does not exist
- Remarks
- ConnectionEvent observers will only be notified upon a change in the state of the connection with the Conformation, e.g. if the Conformation is destroyed or if the connection is being transferred. SUGGESTION: Try to use the Link objects that are returned when attaching observers instead of attaching via this function and watching for ConnectionEvents, as it typically makes connection management easier.
References connection_obs_hub_.
◆ detach_general_obs()
|
inline |
detach GeneralEvent observer function
- Parameters
-
fn pointer to observer's unary member function with signature void( GeneralEvent const & ) ptr RAW pointer to observer object
- Returns
- true if disconnect successful, false if connection does not exist
- Remarks
- GeneralEvent observers will be notified whenever any signal derived from GeneralEvent occurs.
References general_obs_hub_.
◆ detach_identity_obs()
|
inline |
detach IdentityEvent observer function
- Parameters
-
fn pointer to observer's unary member function with signature void( IdentityEvent const & ) ptr RAW pointer to observer object
- Returns
- true if disconnect successful, false if connection does not exist
References identity_obs_hub_.
◆ detach_length_obs()
|
inline |
detach LengthEvent observer function
- Parameters
-
fn pointer to observer's unary member function with signature void( LengthEvent const & ) ptr RAW pointer to observer object
- Returns
- true if disconnect successful, false if connection does not exist
References length_obs_hub_.
◆ detach_xyz_obs()
|
inline |
detach XYZEvent observer function
- Parameters
-
fn pointer to observer's unary member function with signature void( XYZEvent const & ) ptr RAW pointer to observer object
- Returns
- true if disconnect successful, false if connection does not exist
References xyz_obs_hub_.
◆ detached_copy()
|
virtual |
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).
Reimplemented in core::conformation::symmetry::SymmetricConformation, and core::conformation::symmetry::MirrorSymmetricConformation.
References atom_tree_.
Referenced by core::conformation::symmetry::SymmetricConformation::detached_copy().
◆ detect_bonds()
| void core::conformation::Conformation::detect_bonds | ( | ) |
References core::conformation::Residue::atom(), core::chemical::ResidueType::atom_name(), core::chemical::ResidueConnection::atomno(), core::conformation::Residue::atoms(), core::chemical::AtomICoor::build(), core::conformation::Residue::connection_distance(), core::conformation::Residue::connection_incomplete(), core::chemical::AtomICoor::d(), core::conformation::Residue::has_incomplete_connection(), core::chemical::ResidueConnection::icoor(), core::chemical::ResidueType::n_possible_residue_connections(), core::chemical::ResidueType::n_residue_connections_for_atom(), core::conformation::Residue::name(), core::conformation::Residue::nbr_atom(), core::conformation::Residue::nbr_radius(), residue(), core::chemical::ResidueType::residue_connection(), core::conformation::Residue::residue_connection(), residues_, size(), core::conformation::TR(), core::conformation::Residue::type(), core::conformation::Atom::xyz(), and core::conformation::Residue::xyz().
Referenced by protocols::abinitio::ResolutionSwitcher::apply(), protocols::ncbb::oop::OopCreatorMover::apply(), protocols::simple_moves::PeptideStapleMover::apply(), protocols::relax::loop::LoopRelaxMover::apply(), protocols::simple_moves::DeleteChainsMover::apply(), core::pose::symmetry::make_symmetric_pose(), core::io::pose_from_sfr::PoseFromSFRBuilder::refine_pose(), protocols::simple_moves::CyclizationMover::setup_connections(), and protocols::topology_broker::TopologyBroker::switch_to_fullatom().
◆ detect_disulfides() [1/2]
| void core::conformation::Conformation::detect_disulfides | ( | ) |
Detect existing disulfides from the protein structure.
Non-virtual, simply defers to the virtual function with an empty parameter.
Referenced by core::conformation::symmetry::MirrorSymmetricConformation::detect_disulfides().
◆ detect_disulfides() [2/2]
|
virtual |
Detect existing disulfides from the protein structure, using the provided pairs as a starting point.
For full atom confomations, looks at SG-SG distance. If the SG-SG are about 2.02 A apart, calls it a disulfide bond. For centroid and other conformations, the less accurate CB-CB distance is used instead. In this case a CB-CB distance of 3.72 A is optimal.
- Note
- Assumes full atom
Reimplemented in core::conformation::symmetry::SymmetricConformation, and core::conformation::symmetry::MirrorSymmetricConformation.
References add_disulfide_bond(), core::conformation::Residue::atom(), core::conformation::Residue::atom_index(), core::chemical::ResidueType::atom_index(), core::conformation::Residue::atoms(), core::conformation::change_cys_state(), core::chemical::DISULFIDE, core::conformation::find_neighbors(), core::chemical::FULL_ATOM_t, core::chemical::ResidueTypeBase::get_disulfide_atom_name(), core::conformation::Residue::has_variant_type(), core::chemical::ResidueType::is_disulfide_bonded(), core::chemical::ResidueType::is_sidechain_thiol(), core::conformation::Residue::nbr_atom(), core::conformation::Residue::nbr_radius(), core::scoring::pair, residue(), residue_type(), residues_, size(), core::id::to_string(), core::conformation::TR(), core::conformation::Residue::type(), and core::conformation::Atom::xyz().
Referenced by protocols::simple_moves::AddChainMover::add_new_chain(), protocols::simple_moves::WriteSSEMover::apply(), protocols::cryst::MakeLatticeMover::apply(), protocols::cryst::MakeLayerMover::apply(), protocols::frag_picker::nonlocal::NonlocalFrags::apply(), protocols::hybridization::BackboneTorsionPerturbation::apply(), protocols::hybridization::BackboneTorsionSampler::apply(), protocols::indel::IndelOptimizationMover::apply(), protocols::protein_interface_design::movers::LoopMoverFromCommandLine::apply(), protocols::relax::loop::LoopRelaxMover::apply(), protocols::simple_moves::DeleteChainsMover::apply(), protocols::simple_moves::DisulfideInsertionMover::apply(), protocols::simple_moves::SwitchChainOrderMover::apply(), protocols::splice::DesignInterfacesOperation::apply(), protocols::hybridization::HybridizeProtocol::apply(), protocols::hybridization::MRMover::apply(), protocols::splice::Splice::apply(), protocols::analysis::InterfaceAnalyzerMover::apply_const(), protocols::environment::EnvClaimBroker::broker_dofs(), core::import_pose::cleanup(), protocols::fold_from_loops::filters::ScorePoseSegmentFromResidueSelectorFilter::compute(), protocols::grafting::delete_region(), core::pose::symmetry::extract_asymmetric_unit(), protocols::abinitio::AbrelaxApplication::fold(), protocols::simple_moves::CutChainMover::foldTree(), core::pose::initialize_disulfide_bonds(), protocols::simple_moves::AddChainMover::load_pose(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::make_disulfides(), protocols::struct_fragment::StructFragmentMover::make_fragment_picker(), protocols::hybridization::BackboneTorsionPerturbation::perturb(), protocols::hybridization::BackboneTorsionSampler::perturb(), protocols::peptide_deriver::PeptideDeriverFilter::prepare_pose(), protocols::sic_dock::read_biounit(), protocols::grafting::replace_region(), protocols::forge::methods::restore_residues(), protocols::grafting::return_region(), protocols::simple_moves::AddChainMover::swap_chain(), protocols::topology_broker::TopologyBroker::switch_to_fullatom(), protocols::fold_from_loops::utils::Nub::transfer_unfolded_conformation(), and protocols::protein_interface_design::PatchdockReader::transform_pose().
◆ detect_pseudobonds()
| void core::conformation::Conformation::detect_pseudobonds | ( | ) |
References core::conformation::Residue::actual_residue_connection(), add_pseudobond(), core::chemical::ResidueType::atom_name(), core::chemical::ResidueConnection::atomno(), core::conformation::Residue::is_coarse(), core::chemical::ResidueType::n_possible_residue_connections(), core::conformation::Residue::path_distance(), core::chemical::ResConnID::resid(), residue(), residue_(), core::chemical::ResidueType::residue_connection(), core::conformation::Residue::residue_connection(), core::conformation::Residue::residue_connection_conn_id(), core::conformation::Residue::residue_connection_partner(), size(), core::conformation::TR(), and core::conformation::Residue::type().
Referenced by protocols::ncbb::oop::OopCreatorMover::apply(), protocols::simple_moves::DeleteChainsMover::apply(), and core::io::pose_from_sfr::PoseFromSFRBuilder::refine_pose().
◆ dof()
Returns the AtomTree degree of freedom (DOF) <id>
References atom_tree_.
Referenced by protocols::environment::collect_dofs(), core::conformation::is_ideal_position(), core::conformation::symmetry::MirrorSymmetricConformation::set_dof(), and core::conformation::symmetry::SymmetricConformation::set_dof().
◆ dof_id_from_atom_ids() [1/4]
| id::DOF_ID core::conformation::Conformation::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.
References atom_tree_.
◆ dof_id_from_atom_ids() [2/4]
| id::DOF_ID core::conformation::Conformation::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.
References atom_tree_.
◆ dof_id_from_atom_ids() [3/4]
| id::DOF_ID core::conformation::Conformation::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.
References atom_tree_.
Referenced by dof_id_from_atom_ids(), and dof_id_from_torsion_id().
◆ dof_id_from_atom_ids() [4/4]
| id::DOF_ID core::conformation::Conformation::dof_id_from_atom_ids | ( | utility::vector1< id::AtomID > const & | ids | ) | const |
Get the DOF_ID defined by these atoms.
References dof_id_from_atom_ids(), and core::id::GLOBAL_BOGUS_DOF_ID.
◆ dof_id_from_torsion_id()
| id::DOF_ID core::conformation::Conformation::dof_id_from_torsion_id | ( | TorsionID const & | id | ) | const |
Get the DOF_ID corresponding to this TorsionID.
References dof_id_from_atom_ids(), core::id::get_rb_type(), get_torsion_angle_atom_ids(), core::id::GLOBAL_BOGUS_DOF_ID, core::id::JUMP, jump_atom_id(), core::id::TorsionID::rsd(), core::id::TorsionID::torsion(), and core::id::TorsionID::type().
Referenced by atom_tree_torsion(), protocols::simple_moves::SmallMover::dof_id_ranges(), protocols::simple_moves::ShearMover::dof_id_ranges(), protocols::simple_moves::sidechain_moves::SidechainMover::dof_id_ranges(), protocols::simple_moves::sidechain_moves::SidechainMoverBase::dof_id_ranges(), protocols::environment::claims::TorsionClaim::insert_dof_element(), core::optimization::symmetry::SymAtomTreeMinimizer::make_semisymmetric_movemap(), core::pose::symmetry::make_symmetric_movemap(), protocols::environment::ProtectedConformation::set_secstruct(), protocols::environment::ProtectedConformation::set_torsion(), set_torsion(), core::pose::setup_dof_mask_from_move_map(), core::pose::setup_dof_to_torsion_map(), and torsion().
◆ downstream_jump_stub()
| kinematics::Stub core::conformation::Conformation::downstream_jump_stub | ( | int | jump_number | ) | const |
The upstream and downstream Stubs are the coordinate frames between which this jump is transforming.
References atom_tree_, and jump_atom_id().
Referenced by protocols::enzdes::PredesignPerturbMover::apply(), protocols::ligand_docking::RigidSearchMover::apply(), protocols::rigid::RigidBodyPerturbMover::apply(), protocols::rigid::RigidBodyRandomizeMover::apply(), protocols::rigid::RigidBodySpinMover::apply(), protocols::rigid::RigidBodyDeterministicSpinMover::apply(), protocols::rigid::RigidBodyTiltMover::apply(), protocols::rigid::RotateJumpAxisMover::apply(), protocols::simple_moves::UniformRotationMover::apply(), protocols::simple_moves::UniformTranslationMover::apply(), core::kinematics::inverse::calculate_new_jump(), check_valid_membrane(), protocols::ligand_docking::LigandDockProtocol::optimize_orientation3(), protocols::anchored_design::AnchoredDesignMover::perturb_anchor(), and protocols::environment::CoMTrackerCM::update_tracking_residue().
◆ empty()
|
inline |
Returns true if this conformation does not have any residues.
References residues_.
Referenced by residue_typeset_mode().
◆ end() [1/2]
|
inlinenoexcept |
References residues_.
◆ end() [2/2]
|
inlinenoexcept |
◆ fill_missing_atoms()
|
virtual |
Reimplemented in protocols::environment::ProtectedConformation.
References core::kinematics::AtomTree::atom(), core::chemical::ICoorAtomID::atom_id(), core::conformation::Residue::atom_name(), core::conformation::Residue::atom_type(), core::id::AtomID::atomno(), core::id::AtomID::BOGUS_ATOM_ID(), core::conformation::build_residue_tree(), core::chemical::AtomICoor::d(), core::id::D, core::kinematics::AtomTree::dof(), core::id::AtomID_Map< T >::get(), core::conformation::Residue::icoor(), core::kinematics::tree::Atom::input_stub_atom1_id(), core::kinematics::tree::Atom::input_stub_atom2_id(), core::kinematics::tree::Atom::input_stub_atom3_id(), core::chemical::AtomType::is_heavyatom(), core::conformation::Residue::is_virtual(), core::conformation::Residue::name(), core::conformation::Residue::natoms(), core::chemical::AtomICoor::phi(), core::id::PHI, core::io::raw_data::precision(), residue_(), core::conformation::Residue::seqpos(), core::id::AtomID_Map< T >::set(), set_xyz(), size(), core::kinematics::Stub::spherical(), core::chemical::AtomICoor::stub_atom1(), core::chemical::AtomICoor::stub_atom2(), core::chemical::AtomICoor::stub_atom3(), core::chemical::AtomICoor::theta(), core::id::THETA, core::conformation::TR(), core::conformation::Residue::type(), update_residue_coordinates(), xyz(), and core::conformation::Residue::xyz().
Referenced by protocols::antibody::GraftOneCDRLoop::apply(), protocols::antibody_legacy::GraftOneMover::apply(), protocols::indexed_structure_store::apply_residue_entries_to_pose(), core::io::pose_from_sfr::PoseFromSFRBuilder::refine_pose(), and protocols::toolbox::match_enzdes_util::replace_residue_keeping_all_atom_positions().
◆ fix_disulfides()
|
virtual |
Assigns disulfide bonds based on a pre-determined list.
- Note
- works in centroid and full-atom modes
Reimplemented in protocols::environment::ProtectedConformation.
References add_disulfide_bond(), core::chemical::DISULFIDE, and residue().
Referenced by protocols::topology_broker::TopologyBroker::apply(), protocols::calc_taskop_movers::ForceDisulfidesMover::apply(), protocols::relax::loop::LoopRelaxMover::apply(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinMinimizer::apply(), protocols::hybridization::MRMover::apply(), protocols::abinitio::AbrelaxApplication::do_distributed_rerun(), protocols::abinitio::AbrelaxApplication::generate_extended_pose(), core::pose::initialize_disulfide_bonds(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::make_disulfides(), core::io::raw_data::DisulfideFile::read_in_and_set_disulfides(), protocols::fold_from_loops::NubInitioMover::repack_minimize_disulfides(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::setup_disulfides(), protocols::abinitio::AbrelaxApplication::setup_fold(), protocols::topology_broker::TopologyBroker::switch_to_fullatom(), protocols::fold_from_loops::utils::Nub::transfer_unfolded_conformation(), and core::pose::full_model_info::update_disulfides_from_full_model_info().
◆ fold_tree() [1/2]
|
inlinevirtual |
Returns the conformation's FoldTree.
Reimplemented in core::conformation::symmetry::SymmetricConformation.
References fold_tree_.
Referenced by protocols::environment::EnvClaimBroker::add_chainbreak_variants(), core::kinematics::inverse::assert_atoms_are_downstream_of_jump(), core::kinematics::inverse::assert_atoms_are_upstream_of_jump(), core::optimization::symmetry::SymMinimizerMap::asymmetric_dof(), protocols::environment::EnvClaimBroker::broker_fold_tree(), core::conformation::symmetry::SymmetryInfo::dependent_dofs(), core::conformation::symmetry::SymmetryInfo::dof_is_independent(), protocols::simple_moves::asym_fold_and_dock::AsymFoldandDockMoveRbJumpMover::find_new_jump_residue(), core::pose::symmetry::find_new_symmetric_jump_residues(), core::pose::symmetry::find_symmetric_basejump_anchor(), core::conformation::symmetry::SymmetricConformation::fold_tree(), protocols::topology_broker::AsymFoldandDockClaimer::generate_claims(), protocols::topology_broker::FibrilModelingClaimer::generate_claims(), protocols::topology_broker::FoldandDockClaimer::generate_claims(), core::conformation::symmetry::get_asymm_unit_fold_tree(), core::conformation::symmetry::SymmetryInfo::get_dof_derivative_weight(), core::conformation::idealize_position(), protocols::hybridization::HybridizeFoldtreeDynamic::initialize(), insert_conformation_by_jump(), core::conformation::symmetry::MirrorSymmetricConformation::insert_conformation_by_jump(), core::conformation::symmetry::SymmetricConformation::insert_conformation_by_jump(), core::conformation::insert_ideal_bonds_at_polymer_junction(), core::conformation::is_ideal_position(), protocols::membrane::is_membrane_fixed(), protocols::membrane::is_membrane_moveable_by_itself(), core::conformation::symmetry::process_residue_request(), protocols::environment::EnvClaimBroker::render_fold_tree(), protocols::fibril::reorient_extended_fibril(), protocols::simple_ddg::AlaScan::report(), protocols::features::PoseConformationFeatures::report_features_implementation(), protocols::hybridization::HybridizeFoldtreeDynamic::reset(), protocols::environment::ClientMover::sandboxed_copy(), core::conformation::symmetry::set_asymm_unit_fold_tree(), core::conformation::symmetry::set_fold_tree_from_symm_data(), core::conformation::symmetry::MirrorSymmetricConformation::set_jump(), core::conformation::symmetry::setup_symmetric_conformation(), core::conformation::symmetry::symmetrize_fold_tree(), core::conformation::symmetry::MirrorSymmetricConformation::synch_mirror_jumps_with_atomtree(), core::conformation::symmetry::MirrorSymmetricConformation::update_njumps_nres(), and protocols::environment::claims::VirtResClaim::yield_elements().
◆ fold_tree() [2/2]
|
virtual |
Sets the FoldTree to <fold_tree_in>
setup atom tree as well from the fold tree
Reimplemented in core::conformation::symmetry::SymmetricConformation, core::conformation::symmetry::MirrorSymmetricConformation, and protocols::environment::ProtectedConformation.
References annotated_sequence(), core::kinematics::FoldTree::nres(), setup_atom_tree(), size(), core::conformation::TR(), and update_residue_coordinates().
◆ force_update_residue_coordinates()
|
protected |
Force updating of residue coordinates.
Needed by derived classes (particularly MirrorSymmetricConformation).
Needed by derived classes
References residue_coordinates_need_updating_, and update_residue_coordinates().
◆ force_update_residue_torsions()
|
protected |
Force updating of residue torsions.
Needed by derived classes (particularly MirrorSymmetricConformation).
Needed by derived classes
References residue_torsions_need_updating_, and update_residue_torsions().
◆ get_jump_atom_ids()
| bool core::conformation::Conformation::get_jump_atom_ids | ( | core::Size | jump_number, |
| AtomID & | upstream_id, | ||
| AtomID & | downstream_id | ||
| ) | const |
get two atoms connect by jump
References atom_tree_, and jump_atom_id().
Referenced by core::pose::toolbox::AtomLevelDomainMap::get_jump().
◆ get_residue_mask()
|
virtual |
returns a mask of residues to be used in scoring
Returns a mask of residues over which scoring is restricted. Only these residues will be used in constructing the neighbor list.
Reimplemented in core::conformation::symmetry::SymmetricConformation.
References residues_.
Referenced by core::scoring::NeighborList::setup().
◆ get_residue_weight()
|
virtual |
returns a residue-pair weight
Returns a weight to be used when scoring this residue.
Reimplemented in core::conformation::symmetry::SymmetricConformation, and core::conformation::symmetry::MirrorSymmetricConformation.
Referenced by core::scoring::NeighborList::setup().
◆ get_self_ptr() [1/2]
|
inline |
◆ get_self_ptr() [2/2]
|
inline |
self pointers
Referenced by core::conformation::upper_is_symm_equivalent_of_lower().
◆ get_self_weak_ptr() [1/2]
|
inline |
◆ get_self_weak_ptr() [2/2]
|
inline |
Referenced by core::pose::PDBInfo::attach_to().
◆ get_stub_transform()
| kinematics::RT core::conformation::Conformation::get_stub_transform | ( | id::StubID const & | stub_id1, |
| id::StubID const & | stub_id2 | ||
| ) | const |
get the transform between two stubs
References atom_tree_.
Referenced by protocols::forge::build::ConnectRight::extract_rt(), protocols::loophash::get_rt_over_leap_without_foldtree_bs(), and core::fragment::DownJumpSRFD::steal().
◆ get_torsion_angle_atom_ids()
| bool core::conformation::Conformation::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
- Note
- Returns TRUE to signal FAILURE.
References core::id::AtomID::atomno(), backbone_torsion_angle_atoms(), core::id::BB, core::id::BRANCH, branch_connection_torsion_angle_atoms(), core::id::CHI, core::conformation::Residue::chi_atoms(), const_residue_(), core::id::JUMP, core::id::NU, core::conformation::Residue::nu_atoms(), core::id::AtomID::rsd(), core::id::TorsionID::rsd(), core::id::TorsionID::torsion(), torsion(), core::conformation::TR(), and core::id::TorsionID::type().
Referenced by core::pose::rna::add_chi_constraints(), protocols::ncbb::oop::OopCreatorMover::apply(), protocols::symmetry::SetupNCSMover::apply(), protocols::constraint_generator::DihedralConstraintGenerator::apply(), core::optimization::CartesianMinimizerMap::assign_rosetta_torsions_and_trim(), atom_tree_torsion(), bond_orientation(), core::optimization::cartesian_collect_torsional_deriv(), core::scoring::rna::RNA_TorsionPotential::check_intra_residue(), debug_residue_torsions(), dof_id_from_torsion_id(), core::energy_methods::DNA_DihedralEnergy::eval_residue_pair_derivatives(), core::pose::toolbox::AtomLevelDomainMap::get(), core::scoring::rna::RNA_TorsionPotential::get_f1_f2(), core::energy_methods::RNA_SuiteEnergy::get_f1_f2(), core::energy_methods::TNA_SuiteEnergy::get_f1_f2(), core::pose::rna::RNA_IdealCoord::is_torsion_exists(), core::pose::rna::is_torsion_valid(), core::energy_methods::IdealParametersDatabase::lookup_torsion_legacy(), protocols::stepwise::modeler::rna::print_torsion_info(), core::pose::rna::print_torsion_info(), protocols::rna::movers::RNA_LoopCloser::rna_ccd_close(), set_torsion(), and update_residue_torsions().
◆ glycan_tree_set()
| carbohydrates::GlycanTreeSetCOP core::conformation::Conformation::glycan_tree_set | ( | ) | const |
Get the glycan tree set. Nullptr if not present.
Get the glycan tree set. Null if not present.
Rosetta Carbohydrate Data /// Core data for interacting with glycan trees in Rosetta /// /// ///
Rosetta Carbohydrate Data /// Core data for interacting with glycan trees in Rosetta /// ///
References tree_set_observer_.
Referenced by core::conformation::carbohydrates::get_glycosidic_bond_residues(), core::conformation::carbohydrates::get_reference_atoms_for_1st_omega(), core::conformation::carbohydrates::get_reference_atoms_for_2nd_omega(), and insert_conformation_by_jump().
◆ has_passport()
|
inlinevirtual |
Reimplemented in protocols::environment::ProtectedConformation.
◆ in_place_copy()
|
private |
Optimizing the common case of assigning a conformation to another with the same sequence.
References atom_tree_, chain_endings_, dof_moved_, fold_tree_, parameters_set_, residue_coordinates_need_updating_, residue_torsions_need_updating_, residue_type_sets_, residues_, secstruct_, size(), structure_moved_, and xyz_moved_.
Referenced by operator=().
◆ insert_chain_ending()
|
virtual |
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 in protocols::environment::ProtectedConformation.
References chain_endings_, rederive_chain_ids(), and size().
Referenced by protocols::cryst::MakeLatticeMover::add_monomers_to_lattice(), protocols::cryst::MakeLayerMover::add_monomers_to_layer(), protocols::frag_picker::nonlocal::NonlocalFrags::apply(), protocols::grafting::simple_movers::DeleteRegionMover::apply(), protocols::protein_interface_design::movers::AddChainBreak::apply(), protocols::simple_moves::ChainSplitMover::apply(), protocols::metal_interface::MatchGrafter::build_combined_pose_with_zinc_overlay(), core::io::pose_from_sfr::PoseFromSFRBuilder::build_initial_pose(), core::pose::create_subpose(), core::pose::symmetry::extract_asymmetric_unit(), protocols::splice::RBOutMover::get_disulf_jump(), protocols::chemically_conjugated_docking::UBQ_GTPaseMover::initialize(), core::fragment::make_pose_from_frags(), IdentifyLigandMotifs::output_single_motif_to_pdb(), core::io::serialization::read_binary(), protocols::relax::RepeatProteinRelax::setup_repeat_pose(), protocols::relax::RepeatProteinRelax::setup_repeat_pose_jumping(), and protocols::fldsgn::CircularPermutation::split_chains().
◆ insert_conformation_by_jump()
|
virtual |
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 in core::conformation::symmetry::SymmetricConformation, core::conformation::symmetry::MirrorSymmetricConformation, and protocols::environment::ProtectedConformation.
References add_parameters_set(), chain_end(), chain_endings_, core::id::AtomID_Map< T >::clear(), clear_glycan_trees(), core::conformation::Residue::clone(), contains_carbohydrate_residues(), contains_carbohydrate_residues_, dof_moved_, fold_tree(), fold_tree_, glycan_tree_set(), n_parameters_sets(), notify_length_obs(), num_chains(), parameters_set(), pre_nresidue_change(), rederive_chain_ids(), residue(), core::conformation::signals::LengthEvent::RESIDUE_APPEND, residue_cop(), residue_torsions_need_updating_, residues_, core::id::AtomID_Map< T >::resize(), secstruct_, setup_atom_tree(), setup_glycan_trees(), size(), update_sequence_numbering(), and xyz_moved_.
Referenced by protocols::denovo_design::add_residues_to_pose(), protocols::denovo_design::components::append_new_chain_from_template_segment(), core::pose::Pose::append_pose_by_jump(), core::conformation::symmetry::MirrorSymmetricConformation::insert_conformation_by_jump(), core::conformation::symmetry::SymmetricConformation::insert_conformation_by_jump(), protocols::motif_grafting::movers::MotifGraftMover::join_two_poses_by_jump(), and core::conformation::symmetry::setup_symmetric_conformation().
◆ insert_fragment()
|
virtual |
Reimplemented in protocols::environment::ProtectedConformation.
References atom_tree_, and set_dof_moved().
◆ insert_ideal_geometry_at_polymer_bond()
|
virtual |
Set two bond angles and a bond length. DOES NOT DO ANY DIHEDRALS – NOT EVEN OMEGA IF IT'S A PROTEIN
Reimplemented in protocols::environment::ProtectedConformation.
References core::chemical::ICoorAtomID::atomno(), core::id::AtomID::atomno(), core::chemical::AtomICoor::d(), core::chemical::ResidueConnection::icoor(), core::chemical::ResidueType::lower_connect(), core::chemical::ResidueType::mainchain_atom(), core::chemical::ResidueType::mainchain_atoms(), rebuild_polymer_bond_dependent_atoms(), residue_type(), set_bond_angle(), set_bond_length(), core::chemical::AtomICoor::stub_atom1(), core::chemical::AtomICoor::stub_atom2(), core::chemical::AtomICoor::theta(), and core::chemical::ResidueType::upper_connect().
Referenced by protocols::grafting::AnchoredGraftMover::apply(), protocols::grafting::CCDEndsGraftMover::apply(), protocols::forge::components::VarLengthBuild::apply(), protocols::forge::remodel::RemodelMover::apply(), protocols::grafting::idealize_combined_pose(), protocols::chemically_conjugated_docking::UBQ_GTPaseMover::initialize(), protocols::forge::build::SegmentInsert::modify_impl(), protocols::forge::remodel::RemodelLoopMover::repeat_generation_with_additional_residue(), and protocols::forge::remodel::RemodelLoopMover::repeat_propagation().
◆ insert_ideal_geometry_at_residue_connection()
|
virtual |
Set two bond angles and a bond length. DOES NOT DO ANY DIHEDRALS – NOT EVEN OMEGA IF IT'S A PROTEIN
Reimplemented in protocols::environment::ProtectedConformation.
References core::chemical::ICoorAtomID::atomno(), core::chemical::AtomICoor::d(), core::chemical::ResidueConnection::icoor(), rebuild_residue_connection_dependent_atoms(), residues_, set_bond_angle(), set_bond_length(), core::chemical::AtomICoor::stub_atom1(), core::chemical::AtomICoor::stub_atom2(), and core::chemical::AtomICoor::theta().
Referenced by protocols::chemically_conjugated_docking::UBQ_GTPaseMover::initialize().
◆ insert_polymer_residue()
|
private |
insert a polymer residue Fires a LengthEvent::RESIDUE_PREPEND signal.
References atom_tree_, const_residues(), contains_carbohydrate_residues_, fold_tree_, core::conformation::insert_residue_into_atom_tree(), core::chemical::ResidueType::is_carbohydrate(), core::conformation::Residue::is_lower_terminus(), core::conformation::Residue::is_upper_terminus(), notify_length_obs(), pre_nresidue_change(), residue_(), core::conformation::signals::LengthEvent::RESIDUE_PREPEND, residue_torsions_need_updating_, residues_insert(), size(), and core::conformation::Residue::type().
Referenced by append_polymer_residue_after_seqpos(), and prepend_polymer_residue_before_seqpos().
◆ insert_residue_by_bond()
| void core::conformation::Conformation::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() )
insert a residue by bond Fires a LengthEvent::RESIDUE_PREPEND signal.
References core::chemical::ResidueType::atom_index(), atom_tree_, core::conformation::Residue::clone(), const_residues(), fold_tree_, core::conformation::insert_residue_into_atom_tree(), notify_length_obs(), core::conformation::orient_residue_for_ideal_bond(), pre_nresidue_change(), residue_(), core::conformation::Residue::residue_connection(), core::chemical::ResidueType::residue_connection_id_for_atom(), residue_coordinates_need_updating_, core::conformation::signals::LengthEvent::RESIDUE_PREPEND, residue_torsions_need_updating_, residues_, residues_insert(), core::conformation::Residue::seqpos(), size(), core::conformation::Residue::type(), and update_residue_coordinates().
◆ insert_residue_by_jump()
| void core::conformation::Conformation::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() )
insert a residue by jump Fires a LengthEvent::RESIDUE_PREPEND signal.
References atom_tree_, const_residues(), fold_tree_, core::conformation::insert_residue_into_atom_tree(), notify_length_obs(), pre_nresidue_change(), residue_(), core::conformation::signals::LengthEvent::RESIDUE_PREPEND, residue_torsions_need_updating_, residues_insert(), core::conformation::Residue::seqpos(), and size().
Referenced by protocols::membrane::symmetry::SymmetricAddMembraneMover::add_membrane_virtual(), and core::conformation::symmetry::SymmetricConformation::append_residue_by_jump().
◆ inter_residue_connection_partner()
| id::AtomID core::conformation::Conformation::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.
References residues_.
◆ is_bonded()
| bool core::conformation::Conformation::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.
Uses bonded_neighbor_all_res, which iterates through residue connections. To speed up, we would need to turn the connects into a proper bonded graph
References bonded_neighbor_all_res(), and core::id::AtomID::rsd().
Referenced by core::simple_metrics::per_residue_metrics::PerResidueClashMetric::calculate(), and protocols::denovo_design::DisulfidizeMover::find_current_disulfides().
◆ is_centroid()
| bool core::conformation::Conformation::is_centroid | ( | ) | const |
convenience test for residue_type_set mode
References core::chemical::CENTROID_t, and residue_typeset_mode().
Referenced by protocols::environment::EnvClaimBroker::broker_dofs(), and protocols::loop_grower::LoopGrower::get_resrange_hbond_energy().
◆ is_fullatom()
| bool core::conformation::Conformation::is_fullatom | ( | ) | const |
convenience test for residue_type_set mode
References core::chemical::FULL_ATOM_t, and residue_typeset_mode().
Referenced by core::conformation::form_disulfide().
◆ is_membrane()
|
inline |
convenience test for if the conformation contains information for a membrane protein
References membrane_info_.
Referenced by protocols::docking::DockingSlideIntoContact::apply(), protocols::membrane::AddMPLigandMover::apply(), protocols::membrane::OptimizeProteinEmbeddingMover::apply(), protocols::membrane::RandomPositionRotationMover::apply(), protocols::membrane::RandomPositionTranslationMover::apply(), protocols::membrane::SetMembranePositionMover::apply(), protocols::membrane::SetMembraneNormalMover::apply(), protocols::membrane::SetMembraneCenterMover::apply(), protocols::membrane::TransformIntoMembraneMover::apply(), protocols::membrane::TranslationMover::apply(), protocols::membrane::RotationMover::apply(), protocols::membrane::TranslationRotationMover::apply(), protocols::membrane::visualize::VisualizeEmbeddingMover::apply(), protocols::membrane::visualize::VisualizeMembraneMover::apply(), protocols::membrane_benchmark::MembraneEnergyLandscapeSampler::apply(), protocols::membrane_benchmark::PeptideOrientationMover::apply(), protocols::relax::membrane::MPFastRelaxMover::apply(), protocols::membrane::MembranePositionFromTopologyMover::apply(), protocols::relax::membrane::MPRangeRelaxMover::apply(), protocols::relax::RangeRelaxMover::apply(), protocols::symmetric_docking::membrane::MPSymDockMover::apply(), protocols::moves::PyMOLMover::apply(), protocols::docking::DockingEnsemble::calculate_highres_ref_energy(), core::membrane::concave_shell(), protocols::ligand_docking::MinimizeBackbone::create_fold_tree_with_cutpoints(), protocols::ligand_docking::MinimizeBackbone::create_fold_tree_with_ligand_jumps_from_attach_pts(), protocols::membrane::create_membrane_foldtree_anchor_com(), protocols::membrane::create_membrane_foldtree_anchor_pose_tmcom(), protocols::membrane::create_membrane_foldtree_anchor_tmcom(), protocols::membrane::create_membrane_foldtree_from_anchors(), protocols::membrane::create_specific_membrane_foldtree(), protocols::relax::FastRelax::do_minimize(), core::scoring::hbonds::fill_hbond_set(), protocols::membrane::MPLipidAccessibility::fill_up_slices(), protocols::membrane::MPMutateRelaxMover::finalize_setup(), protocols::relax::RangeRelaxMover::finalize_setup(), core::scoring::hbonds::get_membrane_depth_dependent_weight(), core::io::pose_to_sfr::PoseToStructFileRepConverter::grab_membrane_info(), protocols::membrane::is_membrane_fixed(), protocols::membrane::is_membrane_moveable_by_itself(), protocols::membrane::mem_all_atom_rmsd_no_super(), protocols::membrane::mem_all_atom_rmsd_with_super(), protocols::membrane::mem_bb_rmsd_no_super(), protocols::membrane::mem_bb_rmsd_with_super(), core::pose::operator<<(), core::energy_methods::MPHelicalityEnergy::residue_energy(), core::energy_methods::MPCbetaEnergy::residue_energy(), core::energy_methods::MPEnvEnergy::residue_energy(), core::scoring::membrane::MPNonHelixPenalty::residue_energy(), core::scoring::membrane::MPTerminiPenalty::residue_energy(), core::energy_methods::MPPairEnergy::residue_pair_energy(), protocols::membrane::rsd_closest_to_chain_com(), protocols::moves::PyMOLMover::send_membrane_planes(), protocols::membrane::setup_foldtree_from_anchors(), protocols::membrane::setup_foldtree_pose_com(), protocols::relax::membrane::MPFastRelaxMover::setup_relax_foldtree(), and protocols::protein_interface_design::filters::BindingStrainFilter::unbind().
◆ is_mixed_mode()
| bool core::conformation::Conformation::is_mixed_mode | ( | ) | const |
convenience test for residue_type_set mode
References core::chemical::MIXED_t, and residue_typeset_mode().
◆ is_protected()
|
inlinevirtual |
Reimplemented in protocols::environment::ProtectedConformation.
Referenced by protocols::abinitio::abscript::FragmentCM::apply(), and protocols::environment::DofUnlock::~DofUnlock().
◆ jump() [1/2]
| Conformation::Jump const & core::conformation::Conformation::jump | ( | AtomID const & | id | ) | const |
access a jump
References atom_tree_.
◆ jump() [2/2]
| Conformation::Jump const & core::conformation::Conformation::jump | ( | int | jump_number | ) | const |
Returns the Jump with jump number <jump_number>
References atom_tree_, and jump_atom_id().
Referenced by core::kinematics::inverse::calculate_new_jump(), check_valid_membrane(), core::conformation::symmetry::setup_symmetric_conformation(), and core::conformation::symmetry::MirrorSymmetricConformation::synch_mirror_jumps_with_atomtree().
◆ jump_atom_id()
| id::AtomID core::conformation::Conformation::jump_atom_id | ( | int | jump_number | ) | const |
References const_residue_(), core::kinematics::dir_jump, core::kinematics::Edge::downstream_atom(), fold_tree_, core::conformation::get_root_atomno(), core::chemical::has(), core::kinematics::Edge::has_atom_info(), residues_, and core::kinematics::Edge::stop().
Referenced by dof_id_from_torsion_id(), downstream_jump_stub(), get_jump_atom_ids(), jump(), set_jump(), core::conformation::symmetry::MirrorSymmetricConformation::set_jump(), core::conformation::symmetry::SymmetricConformation::set_jump(), protocols::environment::ProtectedConformation::set_jump(), upstream_jump_stub(), protocols::environment::claims::JumpClaim::yield_elements(), and protocols::environment::claims::VirtResClaim::yield_elements().
◆ membrane_info() [1/2]
| membrane::MembraneInfoOP core::conformation::Conformation::membrane_info | ( | ) |
Returns the const MembraneInfo object in conformation.
Returns the MembraneInfo object in conformation.
Membrane Info contains information describing location of the membrane virtual residue in the pose sequence, membrane spanning region definitions and lipid exposure/burial data
References membrane_info_.
Referenced by protocols::simple_filters::SpanTopologyMatchPoseFilter::actual_topology(), protocols::membrane::AddMembraneMover::apply(), protocols::membrane::AqueousPoreFinder::apply(), protocols::membrane::benchmark::SampleTiltAngles::apply(), protocols::membrane::MPLipidAccessibility::apply(), protocols::membrane::RandomPositionTranslationMover::apply(), protocols::membrane::SetMembraneNormalMover::apply(), protocols::membrane::TransformIntoMembraneMover::apply(), protocols::membrane_benchmark::MembraneEnergyLandscapeSampler::apply(), protocols::membrane_benchmark::PeptideOrientationMover::apply(), core::select::residue_selector::ResidueInMembraneSelector::apply(), core::energy_methods::MPHelicalityEnergy::calc_energy(), core::energy_methods::MPResidueLipophilicityEnergy::calc_energy(), core::energy_methods::FaMPEnvSmoothEnergy::calc_energy(), core::energy_methods::MPSpanInsertionEnergy::calc_span_score(), protocols::membrane::check_orientation(), protocols::simple_filters::MembAccesResidueLipophilicityFilter::compute(), protocols::simple_filters::TMsSpanMembraneFilter::compute(), core::conformation::membrane::MembraneGeometry::corrected_xyz(), core::energy_methods::MPSpanInsertionEnergy::create_updated_span(), core::conformation::membrane::MembraneGeometry::f_thickness(), core::conformation::membrane::MembraneGeometry::f_thickness_deriv(), core::conformation::membrane::membrane_geometry::Bicelle::f_transition(), core::conformation::membrane::membrane_geometry::Bicelle::f_transition_deriv(), core::conformation::membrane::membrane_geometry::Bicelle::f_transition_deriv_m(), core::conformation::membrane::membrane_geometry::Bicelle::f_transition_f1(), core::conformation::membrane::membrane_geometry::DoubleVesicle::f_transition_f1(), core::conformation::membrane::membrane_geometry::Bicelle::f_transition_f2(), core::conformation::membrane::membrane_geometry::DoubleVesicle::f_transition_f2(), core::scoring::membrane::MPTMProjPenalty::finalize_total_energy(), core::scoring::hbonds::get_membrane_depth_dependent_weight(), protocols::membrane::scoring::FaWaterToBilayerEnergy::get_menv_params_for_residue(), core::io::pose_to_sfr::PoseToStructFileRepConverter::grab_membrane_info(), core::energy_methods::FaMPEnvEnergy::init(), core::energy_methods::FaMPSolvEnergy::init(), protocols::membrane::membrane_normal_to_length_15(), core::scoring::constraints::MembraneSpanConstraint::MembraneSpanConstraint(), core::scoring::constraints::MembraneSpanTermZConstraint::MembraneSpanTermZConstraint(), core::conformation::membrane::MembraneGeometry::normal_vector(), core::pose::operator<<(), core::conformation::membrane::membrane_geometry::Bicelle::r_alpha(), core::conformation::membrane::membrane_geometry::DoubleVesicle::r_alpha(), core::conformation::membrane::membrane_geometry::Slab::r_alpha(), core::conformation::membrane::membrane_geometry::Vesicle::r_alpha(), core::conformation::membrane::membrane_geometry::Bicelle::r_alpha_m(), core::conformation::membrane::MembraneGeometry::r_alpha_p_z(), core::energy_methods::MPResidueLipophilicityEnergy::report_ressolv(), core::energy_methods::MPCbetaEnergy::residue_energy(), core::energy_methods::MPEnvEnergy::residue_energy(), core::scoring::membrane::MPNonHelixPenalty::residue_energy(), core::scoring::membrane::MPTerminiPenalty::residue_energy(), core::energy_methods::FaMPAsymEzCBEnergy::residue_energy(), core::energy_methods::FaMPAsymEzCGEnergy::residue_energy(), core::energy_methods::MPPairEnergy::residue_pair_energy(), protocols::moves::PyMOLMover::send_membrane_planes(), core::scoring::hbonds::HBondEnergy::setup_for_packing(), core::scoring::hbonds::HBondEnergy::setup_for_scoring(), protocols::simple_filters::SpanTopologyMatchPoseFilter::span_file_topology(), core::conformation::membrane::MembraneGeometry::thickness_vector(), and protocols::membrane::AqueousPoreFinder::update_mp_geo_pore().
◆ membrane_info() [2/2]
| membrane::MembraneInfoOP core::conformation::Conformation::membrane_info | ( | ) | const |
Returns the const MembraneInfo object in conformation.
Returns a Membrane Info Object in the conformation.
Membrane Info contains information describing location of the membrane virtual residue in the pose sequence, membrane spanning region definitions and lipid exposure/burial data
Membrane Info contains information regarding membrane residues, foldtree modifications, fullatom vs. centroid embedding parameters for scoring and the spanning topology/lipids accessibility data
References membrane_info_.
◆ modifiable_residue_type_set_for_conf()
| core::chemical::PoseResidueTypeSetOP core::conformation::Conformation::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.
Return a clone of the Conformation-specific PoseResidueTypeSet. 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.
References core::chemical::FULL_ATOM_t, core::chemical::CacheableResidueTypeSets::get_res_type_set(), core::chemical::INVALID_t, core::chemical::MIXED_t, residue_type_sets_, residue_typeset_mode(), and core::conformation::TR().
Referenced by protocols::drug_design::ApplyChemistryMover::apply(), protocols::ligand_docking::AddHydrogen::apply(), protocols::jd2::ScreeningJobInputter::pose_from_job(), protocols::splice::SampleRotamersFromPDB_RotamerSetOperation::ROT2res(), and core::util::switch_to_residue_type_set().
◆ n_parameters_sets()
| core::Size core::conformation::Conformation::n_parameters_sets | ( | ) | const |
Get the number of parameters sets defined for this Conformation.
References parameters_set_.
Referenced by protocols::helical_bundle::MakeBundle::apply(), protocols::helical_bundle::PerturbBundle::apply(), protocols::helical_bundle::PerturbBundleHelix::apply(), protocols::helical_bundle::BundleParametrizationCalculator::copy_params_from_previous_helices_makebundlehelix_style(), protocols::helical_bundle::BundleReporterFilter::generate_full_tracer_report(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_parametric_info(), and insert_conformation_by_jump().
◆ notify_connection_obs()
|
private |
notify ConnectionEvent observers
work in progress void insert_chemical_chainbreak_between_polymer_residues( Size const lower_seqpos ) { ResidueOP lower_rsd( residues_[ lower_seqpos ] );
the type of the desired variant residue ResidueTypeSet const & rsd_set( lower_rsd->residue_type_set() );
ResidueType const & new_lower_rsd_type ( rsd_set.get_residue_type_with_variant_removed( lower_rsd.type(), UPPER_TERMINUS ) ); ResidueOP new_lower_rsd( ResidueFactory::create_residue( new_lower_rsd_type ) ); }
- Remarks
- called upon a change in the state of connection between the Conformation and the observer (e.g. destruction of Conformation or transfer of connection)
References connection_obs_hub_.
Referenced by clear_observers(), and receive_observers_from().
◆ notify_general_obs()
|
private |
notify GeneralEvent observers
- Remarks
- should only be called when there are no other suitable event types since specific event notifications will automatically fire a GeneralEvent signal
References general_obs_hub_.
Referenced by notify_identity_obs(), notify_length_obs(), and notify_xyz_obs().
◆ notify_identity_obs()
|
private |
notify IdentityEvent observers
- Parameters
-
e the event fire_general fire a GeneralEvent afterwards? default true
References identity_obs_hub_, and notify_general_obs().
Referenced by operator=(), and replace_residue().
◆ notify_length_obs()
|
private |
notify LengthEvent observers
- Parameters
-
e the event fire_general fire a GeneralEvent afterwards? default true
References length_obs_hub_, and notify_general_obs().
Referenced by append_residue(), append_residues(), delete_polymer_residue(), delete_residue_range_slow(), delete_residue_slow(), insert_conformation_by_jump(), insert_polymer_residue(), insert_residue_by_bond(), insert_residue_by_jump(), and operator=().
◆ notify_xyz_obs()
|
private |
notify XYZEvent observers
- Parameters
-
e the event fire_general fire a GeneralEvent afterwards? default true
References notify_general_obs(), and xyz_obs_hub_.
Referenced by operator=(), update_residue_coordinates(), and update_residue_torsions().
◆ num_chains()
|
inline |
Returns the number of chains.
See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.
References chain_endings_.
Referenced by protocols::matdes::SymDofMover::add_components_to_pose_if_necessary(), protocols::chemically_conjugated_docking::add_extra_bodies(), protocols::anchored_design::AnchorMoversData::anchor_noise_constraints_setup(), protocols::dna::SeparateDnaFromNonDna::apply(), protocols::indel::IndelOptimizationMover::apply(), protocols::metal_interface::ZincHeterodimerMover::apply(), protocols::protein_interface_design::movers::PrepackMover::apply(), protocols::protein_interface_design::movers::SetAtomTree::apply(), protocols::seeded_abinitio::SeedFoldTree::apply(), protocols::seeded_abinitio::SegmentHybridizer::apply(), protocols::seeded_abinitio::SwapSegment::apply(), protocols::simple_moves::CyclizationMover::apply(), protocols::simple_moves::SetTorsion::apply(), protocols::simple_moves::SwitchChainOrderMover::apply(), protocols::splice::DesignInterfacesOperation::apply(), protocols::task_operations::PreventChainFromRepackingOperation::apply(), protocols::task_operations::ProteinInterfaceDesignOperation::apply(), protocols::task_operations::RestrictChainToRepackingOperation::apply(), protocols::task_operations::RestrictToInterfaceVectorOperation::apply(), protocols::task_operations::RestrictToTerminiOperation::apply(), protocols::task_operations::SelectBySASAOperation::apply(), protocols::task_operations::SelectResiduesWithinChainOperation::apply(), protocols::enzdes::LigInterfaceEnergyFilter::apply(), protocols::protein_interface_design::movers::BackrubDDMover::apply(), protocols::protein_interface_design::movers::TopologyBrokerMover::apply(), protocols::splice::Splice::apply(), protocols::splice::SpliceOut::apply(), protocols::analysis::InterfaceAnalyzerMover::apply_const(), protocols::splice::SpliceOutAntibody::assign_from_res_to_res(), protocols::splice::SpliceInAntibody::assign_from_res_to_res(), protocols::peptide_deriver::PeptideDeriverMarkdownStreamOutputter::begin_structure(), protocols::denovo_design::components::calc_paired_residues(), chain_begin(), protocols::protein_interface_design::filters::AtomicContactCountFilter::compute(), protocols::indexed_structure_store::filters::FragmentLookupFilter::compute(), protocols::protein_interface_design::filters::RmsdSimpleFilter::compute(), protocols::protein_interface_design::filters::SpecificResiduesNearInterfaceFilter::compute(), protocols::protein_interface_design::filters::SSamountFilter::compute(), protocols::analysis::InterfaceAnalyzerMover::compute_interface_energy(), protocols::simple_filters::SSMotifFinder::compute_jump(), protocols::simple_filters::ResidueIEFilter::compute_resnums(), core::pose::conf2pdb_chain(), protocols::floppy_tail::create_extra_output(), protocols::seeded_abinitio::define_movemap_chains(), protocols::splice::find_residues_on_chain1_inside_interface(), protocols::splice::Splice::fold_tree(), protocols::forge::methods::fold_tree_from_loops(), protocols::forge::methods::fold_tree_from_pose(), protocols::motif_grafting::movers::MotifGraftMover::generate_scaffold_matches(), core::conformation::symmetry::get_chain2range(), protocols::peptide_deriver::PeptideDeriverFilter::get_chain_indices(), core::pack::dunbrack::PeptoidOmegaReporter::get_dof(), protocols::features::InterfaceDdGMover::get_movable_jumps(), protocols::simple_ddg::ddG::get_movable_jumps(), core::pose::has_chain(), protocols::antibody::AntibodyInfo::identify_antibody(), protocols::floppy_tail::FloppyTailMover::init_on_new_input(), protocols::chemically_conjugated_docking::UBQ_GTPaseMover::initialize(), core::pack::dunbrack::PeptoidOmegaReporter::insert_atoms_defining_dof(), insert_conformation_by_jump(), protocols::denovo_design::components::make_lengths_str(), protocols::forge::build::SegmentRebuild::modify_impl(), core::conformation::Residue::orient_onto_residue_peptoid(), protocols::denovo_design::components::pose_matches_description(), protocols::peptide_deriver::PeptideDeriverFilter::prepare_pose(), protocols::cyclic_peptide::PeptideStubMover::preserve_old_mainchain_torsions(), protocols::denovo_design::components::prune_unpaired_residues(), protocols::pose_metric_calculators::ResidueDecompositionByChainCalculator::recompute(), protocols::denovo_design::components::reorder_chains(), protocols::analysis::InterfaceAnalyzerMover::reorder_foldtree_find_jump(), protocols::forge::remodel::RemodelLoopMover::repeat_generation_with_additional_residue(), protocols::forge::remodel::RemodelLoopMover::repeat_propagation(), protocols::denovo_design::components::reverse_chains(), core::io::external::PsiPredInterface::run_psipred(), core::io::external::PsiPredInterface::run_psipred_prob(), protocols::pmut_scan::AlterSpecDisruptionDriver::score(), core::select::residue_selector::ChainSelector::select_chain_by_index(), protocols::protein_interface_design::movers::SetAtomTree::set_ab_fold_tree(), protocols::anchored_design::AnchoredDesignMover::set_fold_tree_and_cutpoints(), protocols::splice::SpliceOut::set_fold_tree_nodes(), protocols::splice::SpliceIn::set_fold_tree_nodes(), protocols::splice::SpliceInAntibody::set_fold_tree_nodes(), protocols::splice::SpliceInTail::set_fold_tree_nodes(), protocols::splice::SpliceOutAntibody::set_fold_tree_nodes(), protocols::splice::SpliceOutTail::set_fold_tree_nodes(), protocols::seeded_abinitio::SeedSetupMover::set_packerTasks_target_and_seeds(), protocols::analysis::InterfaceAnalyzerMover::setup_for_dock_chains(), core::energy_methods::Abego::setup_for_scoring(), protocols::relax::membrane::MPFastRelaxMover::setup_relax_foldtree(), core::conformation::symmetry::setup_symmetric_conformation(), protocols::protein_interface_design::star_fold_tree(), and protocols::splice::Splice::tail_fold_tree().
◆ operator=()
|
virtual |
equals operator
If lengths & sequence of source and target are different, will fire a LengthEvent::INVALIDATE signal and then an IdentityEvent::INVALIDATE signal.
Reimplemented in protocols::environment::ProtectedConformation, core::conformation::symmetry::SymmetricConformation, and core::conformation::symmetry::MirrorSymmetricConformation.
References atom_tree_, chain_endings_, clear(), contains_carbohydrate_residues_, dof_moved_, fold_tree_, in_place_copy(), core::conformation::signals::IdentityEvent::INVALIDATE, core::conformation::signals::LengthEvent::INVALIDATE, membrane_info_, notify_identity_obs(), notify_length_obs(), notify_xyz_obs(), parameters_set_, residue_coordinates_need_updating_, residue_torsions_need_updating_, residue_type_sets_, residues_, secstruct_, sequence_matches(), size(), structure_moved_, tree_set_observer_, and xyz_moved_.
Referenced by protocols::environment::ProtectedConformation::operator=().
◆ parameters_set() [1/2]
| core::conformation::parametric::ParametersSetOP core::conformation::Conformation::parameters_set | ( | core::Size const | index | ) |
Access one of the ParametersSets objects linked to this Conformation.
References parameters_set_.
Referenced by protocols::helical_bundle::MakeBundle::apply(), protocols::helical_bundle::PerturbBundle::apply(), protocols::helical_bundle::PerturbBundleHelix::apply(), protocols::helical_bundle::BundleParametrizationCalculator::copy_params_from_previous_helices_makebundlehelix_style(), protocols::helical_bundle::BundleReporterFilter::generate_full_tracer_report(), core::io::pose_to_sfr::PoseToStructFileRepConverter::get_parametric_info(), and insert_conformation_by_jump().
◆ parameters_set() [2/2]
| core::conformation::parametric::ParametersSetCOP core::conformation::Conformation::parameters_set | ( | core::Size const | index | ) | const |
Const access to one of the ParametersSets objects linked to this Conformation.
References parameters_set_.
◆ pop_passport()
|
inlinevirtual |
Reimplemented in protocols::environment::ProtectedConformation.
Referenced by protocols::environment::DofUnlock::~DofUnlock().
◆ pre_nresidue_change()
|
private |
The Conformation must transfer lazily accumulated "moved" data from the AtomTree before changing the number of residues.
Copy any un-registered coordinate or DOF changes into the existing residues. For now, the AtomTree only tracks which Residues need external coordinate changes, and not internal coordinate changes. When internal coordinates go out-of-date in the atom tree, the "update_internal_coordinates" recursion begins at the root. Moreover, the Conformation updates internal coordinates for all residues when it updates. However, when this changes and the AtomTree starts tracking which residues need to have their internal coordinates updated, then it will be necessary to add a call to update_residue_torsions() here.
References update_residue_coordinates().
Referenced by append_polymer_residue_after_seqpos(), append_residue(), append_residue_by_bond(), append_residue_by_jump(), append_residues(), clear(), delete_polymer_residue(), delete_residue_range_slow(), delete_residue_slow(), insert_conformation_by_jump(), insert_polymer_residue(), insert_residue_by_bond(), insert_residue_by_jump(), prepend_polymer_residue_before_seqpos(), safely_append_polymer_residue_after_seqpos(), and safely_prepend_polymer_residue_before_seqpos().
◆ prepend_polymer_residue_before_seqpos()
|
virtual |
glues to seqpos and perhaps also seqpos-1
Fires a LengthEvent::RESIDUE_PREPEND signal.
Reimplemented in protocols::environment::ProtectedConformation, and core::conformation::symmetry::SymmetricConformation.
References core::conformation::Residue::clone(), dof_moved_, fold_tree_, insert_polymer_residue(), core::conformation::Residue::is_lower_terminus(), core::conformation::Residue::is_upper_terminus(), core::conformation::Residue::lower_connect(), core::conformation::Residue::natoms(), core::conformation::orient_residue_for_ideal_bond(), pre_nresidue_change(), rebuild_polymer_bond_dependent_atoms(), residue_(), size(), core::id::AtomID_Map< T >::size(), core::conformation::Residue::upper_connect(), and xyz_moved_.
Referenced by protocols::protein_interface_design::movers::LoopLengthChange::apply(), core::conformation::idealize_position(), core::conformation::insert_ideal_mainchain_bonds(), core::conformation::symmetry::SymmetricConformation::prepend_polymer_residue_before_seqpos(), and safely_prepend_polymer_residue_before_seqpos().
◆ push_passport()
|
inlinevirtual |
Reimplemented in protocols::environment::ProtectedConformation.
Referenced by protocols::environment::DofUnlock::DofUnlock().
◆ rebuild_polymer_bond_dependent_atoms() [1/2]
|
virtual |
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 in protocols::environment::ProtectedConformation.
Referenced by append_polymer_residue_after_seqpos(), append_residue_by_bond(), core::conformation::insert_ideal_bonds_at_polymer_junction(), insert_ideal_geometry_at_polymer_bond(), core::conformation::symmetry::SymmetricConformation::prepend_polymer_residue_before_seqpos(), prepend_polymer_residue_before_seqpos(), rebuild_polymer_bond_dependent_atoms_this_residue_only(), and update_polymeric_connection().
◆ rebuild_polymer_bond_dependent_atoms() [2/2]
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private |
rebuild atoms in residue seqpos dependent on either the lower (-1) or upper(1) polymer residue
References core::conformation::Residue::atom_depends_on_lower(), core::conformation::Residue::atom_depends_on_upper(), core::conformation::Residue::atom_name(), core::chemical::AtomICoor::build(), core::conformation::Residue::connected_residue_at_lower(), core::conformation::Residue::connected_residue_at_upper(), core::conformation::Residue::icoor(), core::conformation::Residue::is_RNA(), core::conformation::Residue::natoms(), residue_(), set_xyz(), and update_residue_coordinates().
◆ rebuild_polymer_bond_dependent_atoms_this_residue_only()
| void core::conformation::Conformation::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.
References rebuild_polymer_bond_dependent_atoms().
Referenced by protocols::simple_moves::ModifyVariantTypeMover::apply(), protocols::simple_moves::DeclareBond::apply(), protocols::relax::fixH(), and protocols::simple_moves::MutateResidue::make_mutation().
◆ rebuild_residue_connection_dependent_atoms()
| void core::conformation::Conformation::rebuild_residue_connection_dependent_atoms | ( | Size | seqpos, |
| Size | connid | ||
| ) |
- Note
- This could be rewritten to avoid a refold using set_bond_angle, etc might be safer since by-xyz ignores possibility of propagating dependencies from the moving atoms...
References core::chemical::ResidueType::atom_depends_on_connection(), core::chemical::AtomICoor::build(), core::conformation::Residue::connected_residue_at_resconn(), core::conformation::Residue::icoor(), core::conformation::Residue::natoms(), residue_(), set_xyz(), core::conformation::Residue::type(), and update_residue_coordinates().
Referenced by protocols::simple_moves::DeclareBond::apply(), protocols::generalized_kinematic_closure::correct_polymer_dependent_atoms_in_pose_segment(), insert_ideal_geometry_at_residue_connection(), protocols::simple_moves::CyclizationMover::minimize_rebuild(), protocols::simple_moves::CyclizationMover::setup_connections(), protocols::cyclic_peptide::crosslinker::TMA_Helper::update_tma_amide_bond_dependent_atoms_asymmetric(), and protocols::cyclic_peptide::crosslinker::TMA_Helper::update_tma_amide_bond_dependent_atoms_symmetric().
◆ receive_observers_from()
| void core::conformation::Conformation::receive_observers_from | ( | Conformation const & | src | ) |
fire a ConnectionEvent::TRANSFER to transfer observers from some source Conformation
- Parameters
-
src Take observers from this source Conformation.
- Remarks
- Only observers that properly honor the TRANSFER event by re-attaching themselves to 'this' Conformation will be transferred.
References notify_connection_obs(), and core::conformation::signals::ConnectionEvent::TRANSFER.
◆ rederive_chain_endings()
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private |
References chain_endings_, residues_, and size().
Referenced by residues_append(), residues_delete(), and residues_insert().
◆ rederive_chain_ids()
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private |
References chain_endings_, residues_, and size().
Referenced by chain_endings(), chains_from_termini(), delete_chain_ending(), insert_chain_ending(), insert_conformation_by_jump(), reset_chain_endings(), residues_append(), and residues_delete().
◆ replace_residue() [1/2]
|
virtual |
replace residue
replace a residue Fires an IdentityEvent signal.
Reimplemented in core::conformation::symmetry::SymmetricConformation, core::conformation::symmetry::MirrorSymmetricConformation, and protocols::environment::ProtectedConformation.
References atom_tree_, const_residues(), fold_tree_, notify_identity_obs(), core::conformation::replace_residue_in_atom_tree(), core::conformation::signals::IdentityEvent::RESIDUE, residue_torsions_need_updating_, residues_, and residues_replace().
Referenced by protocols::environment::EnvClaimBroker::add_chainbreak_variants(), protocols::stepwise::modeler::packer::SideChainCopier::apply(), core::conformation::change_cys_state(), copy_segment(), core::conformation::form_disulfide_helper(), protocols::residue_optimization::MetapatchEnumeration::generate_derived_types(), core::conformation::idealize_position(), protocols::denovo_design::rebuild_missing_atoms(), protocols::environment::Environment::remove_chainbreak_variants(), core::conformation::replace_conformation_residue_copying_existing_coordinates(), protocols::grafting::replace_region(), core::conformation::symmetry::MirrorSymmetricConformation::replace_residue(), core::conformation::symmetry::SymmetricConformation::replace_residue(), and replace_residue().
◆ replace_residue() [2/2]
|
virtual |
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 in core::conformation::symmetry::SymmetricConformation, core::conformation::symmetry::MirrorSymmetricConformation, and protocols::environment::ProtectedConformation.
References core::conformation::Residue::orient_onto_residue(), replace_residue(), and residues_.
◆ reset_chain_endings()
|
virtual |
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 in protocols::environment::ProtectedConformation.
References chain_endings_, and rederive_chain_ids().
Referenced by protocols::domain_assembly::AssembleLinkerMover::apply(), protocols::loop_grower::FragmentExtension::apply(), and protocols::fldsgn::CircularPermutation::apply().
◆ reset_move_data()
|
virtual |
forget all the structure modifications
called after domain map information is transferred to the Energies class
Reimplemented in protocols::environment::ProtectedConformation.
References dof_moved_, core::id::AtomID_Map< T >::fill_with(), structure_moved_, and xyz_moved_.
◆ reset_residue_type_set_for_conf()
| void core::conformation::Conformation::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.)
Reset the Conformation-specific PoseResidueTypeSet for the appropriat mode to the given RTS.
NOTE: You're potentially in for a bunch of trouble if the passed in set isn't a modified version of the value returned by modifiable_residue_type_set_for_conf() from this conformation. Also, a clone of the RTS is made, so subsequent edits to the RTS will not be reflected in the Conformation's RTS
References core::chemical::INVALID_t, residue_type_set_for_conf(), residue_type_sets_, core::chemical::CacheableResidueTypeSets::set_res_type_set(), and core::conformation::TR().
Referenced by protocols::drug_design::ApplyChemistryMover::apply(), protocols::ligand_docking::AddHydrogen::apply(), core::io::pose_from_sfr::PoseFromSFRBuilder::build_pose(), protocols::jd2::ScreeningJobInputter::pose_from_job(), and core::util::switch_to_residue_type_set().
◆ reset_structure_moved()
|
inline |
reset the structure_moved_ bool
References structure_moved_.
◆ residue()
access one of the residues
- Note
- this access is inlined, since otherwise it shows up in the profiler. This will call non-inlined refold methods if necessary.
update coordinates and torsions for this and all other residues before allowing read access
References residue_coordinates_need_updating_, residue_torsions_need_updating_, residues_, size(), update_residue_coordinates(), and update_residue_torsions().
Referenced by protocols::environment::EnvClaimBroker::add_chainbreak_variants(), core::pose::add_custom_variant_type_to_pose_residue(), core::conformation::add_variant_type_to_conformation_residue(), core::pose::add_variant_type_to_pose_residue(), core::conformation::carbohydrates::align_virtual_atoms_in_carbohydrate_residue(), core::conformation::annotated_atom_graph_from_conformation(), annotated_sequence(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::apply(), protocols::fold_from_loops::movers::NubInitioLoopClosureMover::apply(), protocols::ligand_docking::WriteLigandMolFile::apply(), protocols::protein_interface_design::movers::AddSidechainConstraintsToHotspots::apply(), protocols::protein_interface_design::movers::PlacementAuctionMover::apply(), protocols::protein_interface_design::filters::FilterScanFilter::apply(), protocols::simple_filters::SSMotifFinder::apply(), protocols::simple_filters::StemFinder::apply(), protocols::splice::Splice::apply(), protocols::fold_from_loops::movers::NubInitioLoopClosureMover::apply_closure_trust(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_perturb_backbone_by_bins(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_randomize_backbone_by_bins(), protocols::pockets::PlaidFingerprint::apply_rotation_offset_to_pose_(), protocols::generalized_kinematic_closure::perturber::GeneralizedKICperturber::apply_set_backbone_bin(), protocols::pockets::ElectrostaticpotentialGrid::assign_esp_for_protein_grid_points(), protocols::simple_filters::atom_distance(), core::conformation::atom_graph_from_conformation(), core::conformation::membrane::MembraneInfo::atom_z_position(), protocols::pockets::PocketGrid::autoexpanding_pocket_eval(), bonded_neighbor_all_res(), core::conformation::break_disulfide(), protocols::pockets::PlaidFingerprint::calculate_ligand_CoM(), core::conformation::change_cys_state(), protocols::environment::collect_dofs(), protocols::enzdes::LigBurialFilter::compute(), protocols::protein_interface_design::filters::AverageDegreeFilter::compute(), protocols::simple_filters::AngleToVector::compute(), protocols::simple_filters::ResidueBurialFilter::compute(), protocols::simple_filters::ResidueDistanceFilter::compute(), protocols::simple_filters::ResidueSelectionDistanceFilter::compute(), protocols::simple_filters::SidechainRmsdFilter::compute(), protocols::matdes::OligomericAverageDegreeFilter::compute(), protocols::simple_filters::SSMotifFinder::compute_jump(), protocols::pockets::PlaidFingerprint::compute_ligand_natoms(), protocols::pockets::PlaidFingerprint::compute_ligand_natoms_with_hydrogens(), protocols::ligand_docking::ComputeLigandRDF::compute_rdf(), protocols::star::copy_residues(), copy_segment(), protocols::generalized_kinematic_closure::correct_polymer_dependent_atoms_in_pose_segment(), core::conformation::membrane::MembraneGeometry::corrected_xyz(), core::pose::correctly_add_2prime_connection_variants(), debug_residue_torsions(), declare_chemical_bond(), core::conformation::symmetry::SymmetricConformation::declare_chemical_bond(), core::pose::declare_cutpoint_chemical_bond(), detect_bonds(), detect_disulfides(), core::conformation::symmetry::SymmetricConformation::detect_disulfides(), detect_pseudobonds(), core::conformation::disulfide_bonds(), protocols::environment::dof_id_to_string(), protocols::pockets::PlaidFingerprint::dump_oriented_pose_and_fp_to_pdb(), protocols::viewer::dump_residue_kinemage(), protocols::viewer::dump_structure_kinemage(), protocols::pockets::EggshellGrid::EggshellGrid(), protocols::environment::EXCN_Env_Security_Exception::EXCN_Env_Security_Exception(), core::conformation::carbohydrates::fill_downstream_children_res_and_tips(), protocols::environment::find_implied_cut(), protocols::pockets::PocketGrid::findExemplars(), fix_disulfides(), core::pose::fix_up_residue_type_variants_at_strand_beginning(), core::pose::fix_up_residue_type_variants_at_strand_end(), protocols::splice::Splice::fold_tree(), core::conformation::form_disulfide(), core::conformation::form_disulfide_helper(), core::conformation::carbohydrates::get_carbohydrate_residues_and_tips_of_branch(), core::conformation::carbohydrates::get_distance_to_start(), core::conformation::get_disulf_partner(), core::conformation::carbohydrates::get_downstream_residue_that_this_torsion_moves(), core::scoring::orbitals::OrbitalsScore::get_E_haro_one_way(), core::scoring::orbitals::OrbitalsScore::get_E_hpol_one_way(), core::conformation::carbohydrates::get_glycan_connecting_protein_branch_point(), core::conformation::carbohydrates::get_glycan_start_points(), core::conformation::carbohydrates::get_glycosidic_bond_residues(), core::conformation::carbohydrates::get_glycosidic_TorsionIDs(), core::pose::get_hash_excluding_chain(), core::pose::get_hash_from_chain(), protocols::pockets::GenPharmacophore::get_ideal_hydrogenBond_atoms(), protocols::simple_moves::BackboneMover::get_mainchain_TorsionIDs(), core::conformation::carbohydrates::get_non_NU_TorsionID_from_AtomIDs(), core::scoring::orbitals::OrbitalsScore::get_orb_orb_E(), core::conformation::get_second_atom_from_connection(), core::pose::get_sha1_hash_excluding_chains(), core::pose::get_sha1_hash_from_chains(), core::conformation::symmetry::SymmetricConformation::get_upstream_vrt(), protocols::pockets::PocketGrid::getRelaxResidues(), core::conformation::carbohydrates::has_exocyclic_glycosidic_linkage(), core::conformation::idealize_position(), protocols::pockets::NonPlaidFingerprint::include_eggshell_points_based_on_known_ligand(), protocols::membrane::AddMembraneMover::initialize_membrane_residue(), insert_conformation_by_jump(), core::conformation::symmetry::MirrorSymmetricConformation::insert_conformation_by_jump(), core::conformation::symmetry::SymmetricConformation::insert_conformation_by_jump(), core::conformation::insert_ideal_bonds_at_polymer_junction(), core::conformation::insert_ideal_mainchain_bonds(), core::io::pose_from_sfr::is_connected(), core::conformation::is_disulfide_bond(), core::conformation::carbohydrates::is_glycosidic_omega_torsion(), core::conformation::carbohydrates::is_glycosidic_phi_torsion(), core::conformation::carbohydrates::is_glycosidic_psi_torsion(), core::conformation::is_ideal_position(), protocols::ligand_docking::ComputeLigandRDF::ligand_protein_rdf(), core::scoring::mm::MMBondAngleResidueTypeParamSet::lookup(), protocols::pockets::ElectrostaticpotentialGrid::mark_protein_espGrid_points(), core::conformation::membrane::MembraneInfo::membrane_center(), core::conformation::membrane::MembraneInfo::membrane_normal(), protocols::make_rot_lib::MakeRotLibMover::minimize_rotamer(), protocols::drug_design::ConformationSelectionToRDMol::Mol(), protocols::pockets::PocketGrid::move_pose_to_standard_orie(), core::conformation::membrane::MembraneGeometry::normal_vector(), core::conformation::carbohydrates::GlycanTreeSet::on_length_change(), core::conformation::Residue::orient_onto_residue_peptoid(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::perform_bump_check(), protocols::splice::SpliceOut::place_cut_site_in_segment(), protocols::pockets::PlaidFingerprint::PlaidFingerprint(), protocols::pockets::PocketConstraint::PocketConstraint(), core::conformation::print_atom(), protocols::viewer::print_node(), protocols::ligand_docking::ComputeLigandRDF::protein_protein_rdf(), core::conformation::membrane::membrane_geometry::Bicelle::protein_slice_diameter_at_mem_cen(), core::conformation::membrane::membrane_geometry::Slab::r_alpha(), core::conformation::membrane::MembraneGeometry::r_alpha_p_z(), core::scoring::bin_transitions::BinTransitionCalculator::random_bin_based_on_prev_and_next(), core::scoring::bin_transitions::BinTransitionCalculator::random_mainchain_torsions_from_bin(), core::scoring::bin_transitions::BinTransitionCalculator::random_mainchain_torsions_from_bins(), core::pose::Pose::real_to_virtual(), core::conformation::symmetry::SymmetricConformation::recalculate_transforms(), core::conformation::symmetry::recenter(), protocols::environment::Environment::remove_chainbreak_variants(), core::conformation::remove_variant_type_from_conformation_residue(), core::pose::remove_variant_type_from_pose_residue(), core::conformation::replace_conformation_residue_copying_existing_coordinates(), protocols::simple_filters::res_res_min_distance(), protocols::protein_interface_design::filters::res_rmsd(), protocols::simple_filters::res_rmsd(), core::scoring::func::ConformationXYZ::residue(), core::conformation::symmetry::residue_center_of_mass(), residue_data(), core::conformation::residue_point_graph_from_conformation(), core::conformation::membrane::MembraneInfo::residue_z_position(), core::conformation::symmetry::return_nearest_residue(), protocols::pockets::PlaidFingerprint::rmsd(), core::pose::symmetry::sealed_symmetric_fold_tree(), sequence_matches(), core::conformation::symmetry::set_fold_tree_from_symm_data(), protocols::pockets::PocketConstraint::set_target_res(), protocols::pockets::PocketConstraint::set_target_res_pdb(), protocols::star::setup_constraints(), protocols::medal::setup_coordinate_constraints(), core::energy_methods::Abego::setup_for_scoring(), core::conformation::carbohydrates::GlycanTree::setup_glycan_nodes(), core::pose::show_adjacent_nt_connections(), core::io::pose_from_sfr::show_residue_connections(), protocols::protein_interface_design::movers::PlaceStubMover::StubMinimize(), core::conformation::membrane::MembraneGeometry::thickness_vector(), protocols::calc_taskop_filters::RelativePoseFilter::thread_seq(), torsion(), core::conformation::carbohydrates::GlycanNode::update_connectivity_data(), core::conformation::update_cutpoint_virtual_atoms_if_connected(), core::conformation::symmetry::SymmetricConformation::update_noncanonical_connection(), core::conformation::carbohydrates::GlycanTree::update_on_length_change(), core::conformation::symmetry::MirrorSymmetricConformation::update_residue_identities(), core::kinematics::jacobian::ModuleType1::update_screw_vectors(), core::pose::Pose::virtual_to_real(), core::conformation::ConformationKinWriter::write_coords(), protocols::environment::claims::TorsionClaim::yield_elements(), and protocols::environment::claims::XYZClaim::yield_elements().
◆ residue_()
Returns a non-constant residue reference without triggering coordinate/torsion update.
Use with care. Useful inside torsion/coordinate setters where we want chemical info about a given residue but don't want to trigger the coordinate/torsion updates that go along with a call to residue(seqpos).
- Note
- APL – Conformation should not give out non-const access to its residues even to derived classes. This function should not be called by derived classes.
References residues_, and size().
Referenced by append_polymer_residue_after_seqpos(), append_residue_by_bond(), append_residues(), apply_transform_Rx_plus_v(), detect_pseudobonds(), fill_missing_atoms(), insert_polymer_residue(), insert_residue_by_bond(), insert_residue_by_jump(), prepend_polymer_residue_before_seqpos(), rebuild_polymer_bond_dependent_atoms(), rebuild_residue_connection_dependent_atoms(), residue_data(), set_polymeric_connection(), and sever_chemical_bond().
◆ residue_cop()
|
inline |
access one of the residues, using COP
References residue_coordinates_need_updating_, residue_torsions_need_updating_, residues_, size(), update_residue_coordinates(), and update_residue_torsions().
Referenced by protocols::helical_bundle::MakeBundleHelix::add_parameter_info_to_pose(), core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyVoxelGrid::compute_total_volume_of_current_residues(), core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyVoxelGrid::compute_volumes_of_buried_rotamers(), core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNode::detect_intra_residue_hydrogen_bonds_symmetric(), core::pack::guidance_scoreterms::hbnet_energy::HBNetEnergy::finalize_total_energy(), core::pack::interaction_graph::generate_rotamers_from_packer_solution_description(), core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty::initialize_curstate_graph(), core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::initialize_graph_for_packing(), insert_conformation_by_jump(), core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::provide_pymol_commands_to_show_groups(), core::pack::guidance_scoreterms::voids_penalty_energy::VoidsPenaltyVoxelGrid::prune_voxels_for_fixed_residues(), protocols::loop_grower::transform_to_closest_symmunit(), and core::conformation::parametric::ParametersSet::update_residue_links().
◆ residue_data() [1/2]
|
inline |
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.
The purpose of the residue-level data cache is so that scoring terms may store coordinate-derived information in a Residue (perhaps a Residue that does not belong to a Conformation) so that it can be used during scoring evaluation. Accessing the residue_data will trigger a coordinate (or torsion) update.
References core::conformation::Residue::nonconst_data_ptr(), residue_(), residue_coordinates_need_updating_, residue_torsions_need_updating_, size(), update_residue_coordinates(), and update_residue_torsions().
◆ residue_data() [2/2]
|
inline |
Read access to the datacache array stored inside a Residue object. Also accessible to the user by calling residue( seqpos ).data_ptr() directly.
The purpose of the residue-level data cache is so that scoring terms may store coordinate-derived information in a Residue (perhaps a Residue that does not belong to a Conformation) so that it can be used during scoring evaluation.
References core::conformation::Residue::data_ptr(), and residue().
◆ residue_type()
|
inline |
access one of the residue's types – avoids coord/torsion update
References residues_, and size().
Referenced by add_disulfide_bond(), core::conformation::annotated_atom_graph_from_conformation(), protocols::simple_moves::AddJobPairData::apply(), core::conformation::symmetry::SymmetricConformation::apply_transform_Rx_plus_v(), core::conformation::atom_graph_from_conformation(), core::chemical::ICoorAtomID::atom_id(), core::conformation::symmetry::calculate_inverting_virtuals(), core::conformation::change_cys_state(), protocols::ligand_docking::ComputeLigandRDF::compute_rdf(), detect_disulfides(), core::conformation::symmetry::SymmetricConformation::detect_disulfides(), core::kinematics::jacobian::SeriesJacobians::determine_residue_series_type(), core::conformation::form_disulfide(), core::conformation::form_disulfide_helper(), core::pose::initialize_atomid_map(), core::pose::initialize_atomid_map_heavy_only(), insert_ideal_geometry_at_polymer_bond(), core::conformation::Residue::inter_residue_connection_partner(), core::scoring::mm::MMBondAngleResidueTypeParamSet::lookup(), protocols::drug_design::ConformationSelectionToRDMol::Mol(), protocols::viewer::print_node(), core::conformation::symmetry::recenter(), protocols::fibril::reorient_extended_fibril(), and residue_typeset_mode().
◆ residue_type_ptr()
|
inline |
◆ residue_type_set_for_conf()
| core::chemical::ResidueTypeSetCOP core::conformation::Conformation::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.
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.
References core::chemical::FULL_ATOM_t, core::chemical::CacheableResidueTypeSets::get_res_type_set(), core::chemical::INVALID_t, core::chemical::MIXED_t, residue_type_sets_, residue_typeset_mode(), and core::conformation::TR().
Referenced by protocols::environment::EnvClaimBroker::add_chainbreak_variants(), core::conformation::add_variant_type_to_conformation_residue(), core::conformation::change_cys_state(), core::scoring::RamaPrePro::eval_rpp_rama_derivatives(), core::scoring::RamaPrePro::eval_rpp_rama_score(), core::conformation::symmetry::MirrorSymmetricConformation::flip_chirality(), core::conformation::form_disulfide(), core::scoring::RamaPrePro::get_mainchain_torsions_covered(), core::conformation::inv_virtual_type_for_conf(), core::scoring::RamaPrePro::random_mainchain_torsions(), core::conformation::remove_variant_type_from_conformation_residue(), reset_residue_type_set_for_conf(), core::pose::Pose::residue_type_set_for_pose(), core::conformation::symmetry::setup_symmetric_conformation(), and core::conformation::virtual_type_for_conf().
◆ residue_typeset_mode()
| core::chemical::TypeSetMode core::conformation::Conformation::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.
References empty(), core::chemical::INVALID_t, core::chemical::MIXED_t, residue_type(), size(), core::conformation::TR(), and core::chemical::TYPE_SET_MODES_LENGTH.
Referenced by protocols::toolbox::match_enzdes_util::AlignPoseToInvrotTreeMover::apply(), protocols::loop_grower::LoopPartialSolution::apply(), protocols::comparative_modeling::ThreadingMover::apply(), protocols::forge::components::VarLengthBuild::apply(), protocols::loop_grower::LoopPartialSolution::apply_sheets(), protocols::forge::remodel::RemodelMover::centroid_build(), protocols::loop_grower::LoopGrower::get_resrange_hbond_energy(), core::pose::get_restype_for_pose(), core::conformation::inv_virtual_type_for_conf(), is_centroid(), is_fullatom(), is_mixed_mode(), modifiable_residue_type_set_for_conf(), protocols::loop_grower::LoopGrower::nton3_hbond_score(), protocols::comparative_modeling::rebuild_loops_until_closed(), residue_type_set_for_conf(), and core::conformation::virtual_type_for_conf().
◆ residues_append()
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private |
PRIVATE: wrap direct access to the Residues container for appending
- Warning
- Since this is the innermost routine when replacing a residue, it does not fire any signals to ensure that observer access to the residues container does not trigger an atom tree refold prematurely.
References core::id::NamedAtomID::atom(), core::id::NamedAtomID::BOGUS_NAMED_ATOM_ID(), core::conformation::Residue::clone(), dof_moved_, core::conformation::Residue::natoms(), rederive_chain_endings(), rederive_chain_ids(), residues_, core::id::AtomID_Map< T >::resize(), core::id::NamedAtomID::rsd(), secstruct_, structure_moved_, core::conformation::TR(), update_noncanonical_connection(), update_polymeric_connection(), and xyz_moved_.
Referenced by append_residue().
◆ residues_delete()
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private |
PRIVATE: wrap direct access to the Residues container for replacement also handles redimensioning and setting of the _moved arrays and updating of sequence numbers
- Warning
- Since this is the innermost routine when replacing a residue, it does not fire any signals to ensure that observer access to the residues container does not trigger an atom tree refold prematurely.
References rederive_chain_endings(), rederive_chain_ids(), residues_, secstruct_, update_polymeric_connection(), and update_sequence_numbering().
Referenced by delete_polymer_residue(), delete_residue_range_slow(), and delete_residue_slow().
◆ residues_insert()
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private |
PRIVATE: wrap direct access to the Residues container for replacement also handles redimensioning and setting of the _moved arrays and updating of sequence numbers
- Warning
- Since this is the innermost routine when replacing a residue, it does not fire any signals to ensure that observer access to the residues container does not trigger an atom tree refold prematurely.
References core::conformation::Residue::clone(), dof_moved_, core::conformation::Residue::name(), core::conformation::Residue::natoms(), rederive_chain_endings(), residues_, secstruct_, structure_moved_, update_polymeric_connection(), update_sequence_numbering(), and xyz_moved_.
Referenced by insert_polymer_residue(), insert_residue_by_bond(), and insert_residue_by_jump().
◆ residues_replace()
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private |
wrap direct access to the Residues container
PRIVATE: wrap direct access to the Residues container for replacement also handles redimensioning and setting of the _moved arrays
- Warning
- Since this is the innermost routine when replacing a residue, it does not fire any signals to ensure that observer access to the residues container does not trigger an atom tree refold prematurely.
References core::conformation::Residue::clone(), dof_moved_, core::conformation::Residue::natoms(), residues_, structure_moved_, and xyz_moved_.
Referenced by replace_residue().
◆ resolve_partial_atom_id()
| id::AtomID core::conformation::Conformation::resolve_partial_atom_id | ( | id::PartialAtomID const & | partial_id | ) | const |
Resolve a partial atom ID into an AtomID that is specific for this Conformation.
References const_residue_(), core::conformation::Residue::resolve_partial_atom_id(), and core::id::PartialAtomID::rsd().
Referenced by core::optimization::activate_dof_deriv_terms_for_cart_min().
◆ safely_append_polymer_residue_after_seqpos()
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virtual |
glues to seqpos and perhaps also seqpos+1, removes termini variants if necessary
Reimplemented in protocols::environment::ProtectedConformation, and core::conformation::symmetry::SymmetricConformation.
References append_polymer_residue_after_seqpos(), pre_nresidue_change(), and core::conformation::remove_upper_terminus_type_from_conformation_residue().
Referenced by protocols::loop_grower::LoopPartialSolution::add_sheets(), protocols::seeded_abinitio::GrowPeptides::append_residues_cterminally(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::apply(), protocols::loop_grower::SheetSampler::apply(), protocols::ncbb::oop::OopCreatorMover::apply(), protocols::fldsgn::CircularPermutation::apply(), protocols::forge::components::VarLengthBuild::apply(), protocols::forge::remodel::RemodelMover::apply(), protocols::loops::apply_sequence_mapping(), protocols::fold_from_loops::utils::attach_unfolded_pose_to_pose_c_term(), protocols::loop_grower::LoopComparator::fill_pose(), protocols::forge::methods::grow_right_r(), core::conformation::is_ideal_position(), protocols::protein_interface_design::movers::PlaceOnLoop::loop_length(), protocols::forge::remodel::RemodelLoopMover::repeat_generation_with_additional_residue(), protocols::ub_e2c::ubi_e2c_modeler::restore_cter(), protocols::loop_grower::LoopGrower::single_grow(), and protocols::loop_grower::LoopGrower::update_to_stored().
◆ safely_prepend_polymer_residue_before_seqpos()
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virtual |
glues to seqpos and perhaps also seqpos-1, removes termini variants if necessary
Fires a LengthEvent::RESIDUE_PREPEND signal.
Reimplemented in protocols::environment::ProtectedConformation, and core::conformation::symmetry::SymmetricConformation.
References pre_nresidue_change(), prepend_polymer_residue_before_seqpos(), and core::conformation::remove_lower_terminus_type_from_conformation_residue().
Referenced by protocols::loop_grower::LoopPartialSolution::add_sheets(), protocols::seeded_abinitio::GrowPeptides::append_residues_nterminally(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::apply(), protocols::loop_grower::SheetSampler::apply(), protocols::ncbb::oop::OopCreatorMover::apply(), protocols::protein_interface_design::movers::LoopLengthChange::apply(), protocols::loops::apply_sequence_mapping(), protocols::fold_from_loops::utils::attach_unfolded_pose_to_pose_n_term(), protocols::splice::SpliceOut::build_ideal_segment(), protocols::splice::SpliceIn::build_ideal_segment(), protocols::splice::SpliceInTail::build_ideal_segment(), protocols::splice::SpliceOutTail::build_ideal_segment(), protocols::loop_grower::LoopComparator::fill_pose(), protocols::forge::methods::grow_left_r(), core::conformation::is_ideal_position(), protocols::loop_grower::LoopGrower::single_grow(), and protocols::loop_grower::LoopGrower::update_to_stored().
◆ same_type_as_me()
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virtual |
determine the type of the ConformationOP
Reimplemented in core::conformation::symmetry::SymmetricConformation, core::conformation::symmetry::MirrorSymmetricConformation, and protocols::environment::ProtectedConformation.
References same_type_as_me().
Referenced by core::import_pose::pose_from_file(), protocols::environment::ProtectedConformation::same_type_as_me(), same_type_as_me(), core::conformation::symmetry::MirrorSymmetricConformation::same_type_as_me(), and core::conformation::symmetry::SymmetricConformation::same_type_as_me().
◆ secstruct()
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inline |
Returns the secondary structure the position <seqpos>
- Returns
- character representing secondary structure; returns 'L' if the requested sequence position is larger than the length in the secondary structure array
References secstruct_.
Referenced by protocols::loophash::LoopHashDiversifier::apply(), protocols::LoopRebuild::fast_ccd_close_loops(), protocols::loops::loop_mover::perturb::fast_ccd_close_loops(), protocols::membrane::get_secstruct(), core::scoring::SecondaryStructurePotential::identify_ss(), core::scoring::MembranePotential::non_helix_in_membrane_penalty(), core::energy_methods::EnvEnergy::residue_energy(), core::scoring::membrane::MPNonHelixPenalty::residue_energy(), and core::energy_methods::CenPairEnergy::residue_pair_energy().
◆ sequence_matches()
| bool core::conformation::Conformation::sequence_matches | ( | Conformation const & | other | ) | const |
do the names of all residues in this and src match?
Am I composed of the same sequence of ResidueType objects as other? DANGER! Fails, unexpectedly, if a histidine pair has a different tautomerization. tex, 9/12/08 The above comment points out that this method isn't a clearly defined idea, because there are many ways that someone could imagine comparing the a sequence, including:
- cutpoint variants
- tautomers
- disulfides For some applications, it's probably to get strings of the one-letter names of the sequence and compare those instead.
References core::conformation::Residue::chain(), residue(), size(), and core::conformation::Residue::type().
Referenced by operator=(), protocols::design_opt::GreedyOptMutationMover::pose_coords_are_same(), and protocols::matdes::MatDesGreedyOptMutationMover::pose_coords_are_same().
◆ set_bond_angle()
|
virtual |
Sets the bond angle defined by <atom[1-3]> to <setting>
- Note
- in radians!!
Reimplemented in core::conformation::symmetry::SymmetricConformation, and protocols::environment::ProtectedConformation.
References align_virtual_atoms_in_carbohydrate_residue(), atom_tree_, residues_, core::id::AtomID::rsd(), set_dof_moved(), and core::id::DOF_ID::valid().
Referenced by protocols::farnesyl::InstallFarnesylMover::apply(), core::fragment::BBTorsionAndAnglesSRFD::apply(), protocols::kinematic_closure::ClosureProblem::apply_internal_coordinates(), protocols::backbone_moves::local_backbone_mover::Residue::apply_to_pose(), protocols::helical_bundle::copy_helix_bondangles(), protocols::simple_moves::RepeatPropagationMover::copy_phi_psi_omega(), protocols::cyclic_peptide::crosslinker::correct_thioether_virtuals(), protocols::abinitio::abscript::fix_internal_coords_of_siblings(), protocols::topology_broker::fix_internal_coords_of_siblings(), protocols::abinitio::abscript::fix_mainchain_connect(), protocols::topology_broker::fix_mainchain_connect(), core::conformation::idealize_position(), core::conformation::insert_ideal_bonds_at_polymer_junction(), insert_ideal_geometry_at_polymer_bond(), insert_ideal_geometry_at_residue_connection(), core::conformation::insert_ideal_mainchain_bonds(), protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::semiexpl_water_hbgeom_score(), core::conformation::symmetry::SymmetricConformation::set_bond_angle(), and protocols::generalized_kinematic_closure::set_loop_pose().
◆ set_bond_length()
|
virtual |
Sets the cond length between <atom1> and <atom2> to <setting>
Reimplemented in core::conformation::symmetry::SymmetricConformation, and protocols::environment::ProtectedConformation.
References align_virtual_atoms_in_carbohydrate_residue(), atom_tree_, residues_, core::id::AtomID::rsd(), set_dof_moved(), and core::id::DOF_ID::valid().
Referenced by protocols::farnesyl::InstallFarnesylMover::apply(), protocols::kinematic_closure::ClosureProblem::apply_internal_coordinates(), protocols::backbone_moves::local_backbone_mover::Residue::apply_to_pose(), protocols::helical_bundle::copy_helix_bondlengths(), protocols::simple_moves::RepeatPropagationMover::copy_phi_psi_omega(), protocols::cyclic_peptide::crosslinker::correct_thioether_virtuals(), protocols::abinitio::abscript::fix_mainchain_connect(), protocols::topology_broker::fix_mainchain_connect(), core::conformation::idealize_position(), core::conformation::insert_ideal_bonds_at_polymer_junction(), insert_ideal_geometry_at_polymer_bond(), insert_ideal_geometry_at_residue_connection(), core::conformation::insert_ideal_mainchain_bonds(), protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::semiexpl_water_hbgeom_score(), core::conformation::symmetry::SymmetricConformation::set_bond_length(), and protocols::generalized_kinematic_closure::set_loop_pose().
◆ set_dof()
Sets the AtomTree degree of freedom (DOF) <id> to <setting>
Reimplemented in core::conformation::symmetry::SymmetricConformation, core::conformation::symmetry::MirrorSymmetricConformation, and protocols::environment::ProtectedConformation.
References atom_tree_, residue_torsions_need_updating_, and set_dof_moved().
Referenced by protocols::abinitio::abscript::fix_internal_coords_of_siblings(), protocols::topology_broker::fix_internal_coords_of_siblings(), core::conformation::symmetry::MirrorSymmetricConformation::set_dof(), and core::conformation::symmetry::SymmetricConformation::set_dof().
◆ set_dof_moved() [1/2]
|
inlineprivate |
notify of dof-change
References dof_moved_, residue_coordinates_need_updating_, and structure_moved_.
Referenced by insert_fragment(), set_bond_angle(), set_bond_length(), set_dof(), set_jump(), set_stub_transform(), set_torsion(), and set_torsion_angle().
◆ set_dof_moved() [2/2]
|
inlineprivate |
notify of dof-change
References dof_moved_, residue_coordinates_need_updating_, and structure_moved_.
◆ set_jump() [1/2]
|
virtual |
set a jump
Reimplemented in core::conformation::symmetry::SymmetricConformation, core::conformation::symmetry::MirrorSymmetricConformation, and protocols::environment::ProtectedConformation.
References atom_tree_, core::kinematics::Jump::ortho_check(), and set_dof_moved().
◆ set_jump() [2/2]
|
virtual |
Sets the jump <jump_number> to <new_jump>
Reimplemented in protocols::environment::ProtectedConformation, core::conformation::symmetry::SymmetricConformation, and core::conformation::symmetry::MirrorSymmetricConformation.
References atom_tree_, jump_atom_id(), core::kinematics::Jump::ortho_check(), and set_dof_moved().
Referenced by protocols::forge::remodel::RemodelLoopMover::repeat_generation_with_additional_residue(), protocols::environment::ProtectedConformation::set_jump(), core::conformation::symmetry::MirrorSymmetricConformation::set_jump(), core::conformation::symmetry::SymmetricConformation::set_jump(), and core::conformation::symmetry::MirrorSymmetricConformation::synch_mirror_jumps_with_atomtree().
◆ set_jump_atom_stub_id()
| void core::conformation::Conformation::set_jump_atom_stub_id | ( | id::StubID const & | id | ) |
References atom_tree_.
◆ set_membrane_info()
| void core::conformation::Conformation::set_membrane_info | ( | membrane::MembraneInfoOP | mem_info | ) |
Setup a Membrane Info object in Conformation - pos & topology.
Rosetta Membrane Framework /// Core data for interacting with membrane proteins in Rosetta /// /// Authors: ///
- Rebecca Alford (rfalford12@gmail.com) ///
- Julia Koehler Leman (julia.koehler1982@gmail.com) ///
Jeff Gray (jgray@jhu.edu) ///
Add a MembraneInfo object - describes the position of the membrane virtual residue, information on membrane spanning regions, lipid exposure/burial of residues in the pose, and fullatom steepness and thickness parameters. At construction, specify membrane position and list of spanning topology objects by chain.
Add a MembraneInfo object - describes the position of the membrane virtual residue, information on membrane spanning regions, lipid exposure/burial of residues in the pose, and fullatom steepness and thickness parameters. At construction, specify membrane position and list of spanning topology objects by chain.
References membrane_info_.
Referenced by protocols::membrane::AddMembraneMover::apply().
◆ set_noncanonical_connection()
| void core::conformation::Conformation::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.
References residues_.
Referenced by protocols::simple_moves::DeclareBond::apply(), update_noncanonical_connection(), and core::conformation::symmetry::SymmetricConformation::update_noncanonical_connection().
◆ set_polymeric_connection()
|
virtual |
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 in protocols::environment::ProtectedConformation.
References residue_(), residues_, core::conformation::TR(), core::conformation::Residue::type(), and core::chemical::ResidueType::upper_connect_id().
Referenced by update_polymeric_connection().
◆ set_secstruct()
|
inlinevirtual |
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 in core::conformation::symmetry::SymmetricConformation, and protocols::environment::ProtectedConformation.
References secstruct_.
Referenced by protocols::environment::ProtectedConformation::set_secstruct(), and core::conformation::symmetry::SymmetricConformation::set_secstruct().
◆ set_stub_transform()
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virtual |
Set the transform between two stubs – only works if there's a jump between the two sets of stubatoms.
Reimplemented in protocols::environment::ProtectedConformation.
References atom_tree_, and set_dof_moved().
Referenced by protocols::denovo_design::movers::AlignResiduesMover::align_residues(), core::fragment::DownJumpSRFD::apply(), core::io::silent::BinarySilentStruct::fill_pose(), core::io::silent::ProteinSilentStruct_Template< T >::fill_pose(), protocols::forge::build::ConnectRight::modify_impl(), protocols::jumping::MembraneJump::rt_templates(), protocols::jumping::PairingLibrary::set_tmh_jump(), and core::pose::swap_transform().
◆ set_torsion()
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virtual |
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 in core::conformation::symmetry::SymmetricConformation, core::conformation::symmetry::MirrorSymmetricConformation, and protocols::environment::ProtectedConformation.
References atom_tree_, core::id::BB, core::id::BRANCH, core::id::CHI, dof_id_from_torsion_id(), get_torsion_angle_atom_ids(), core::id::JUMP, core::conformation::Residue::mainchain_atom(), core::conformation::Residue::mainchain_atoms(), core::conformation::Residue::mainchain_torsions(), core::id::NU, core::id::PHI, residues_, core::id::TorsionID::rsd(), set_dof_moved(), core::id::TorsionID::torsion(), core::conformation::TR(), core::id::TorsionID::type(), and core::id::DOF_ID::valid().
Referenced by protocols::loops::loop_closure::kinematic_closure::KinematicMover::apply(), protocols::simple_moves::RandomOmegaFlipMover::apply(), protocols::simple_moves::RandomTorsionMover::apply(), core::kinematics::jacobian::ModuleType1::apply_delta_torsion_values(), protocols::helical_bundle::copy_helix_dihedrals(), core::conformation::idealize_position(), protocols::environment::ProtectedConformation::set_torsion(), core::conformation::symmetry::MirrorSymmetricConformation::set_torsion(), core::conformation::symmetry::SymmetricConformation::set_torsion(), and core::kinematics::jacobian::ModuleType1::set_torsion_values().
◆ set_torsion_angle()
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virtual |
Sets the torsion angle defined by <atom[1-4]> to <setting>
Reimplemented in core::conformation::symmetry::SymmetricConformation, core::conformation::symmetry::MirrorSymmetricConformation, and protocols::environment::ProtectedConformation.
References align_virtual_atoms_in_carbohydrate_residue(), atom_tree_, residue_torsions_need_updating_, residues_, core::id::AtomID::rsd(), set_dof_moved(), core::conformation::TR(), and core::id::DOF_ID::valid().
Referenced by protocols::simple_moves::oop::OopMover::apply(), protocols::simple_moves::triazolamer::TriazolamerMover::apply(), protocols::simple_moves::chiral::ChiralMover::apply(), protocols::simple_moves::SetTorsion::apply(), protocols::simple_moves::TorsionDOFMover::apply(), protocols::abinitio::abscript::fix_mainchain_connect(), protocols::topology_broker::fix_mainchain_connect(), protocols::generalized_kinematic_closure::general_set_phi(), protocols::generalized_kinematic_closure::general_set_psi(), protocols::chemically_conjugated_docking::UBQ_GTPaseMover::initialize(), protocols::frags::TorsionFragment::insert(), protocols::cyclic_peptide::PeptideStubMover::preserve_old_mainchain_torsions(), protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::semiexpl_water_hbgeom_score(), core::conformation::carbohydrates::set_glycosidic_torsion(), protocols::generalized_kinematic_closure::set_loop_pose(), core::conformation::symmetry::MirrorSymmetricConformation::set_torsion_angle(), core::conformation::symmetry::SymmetricConformation::set_torsion_angle(), protocols::simple_moves::oop::OopMover::update_hydrogens_(), and protocols::simple_moves::triazolamer::TriazolamerMover::update_hydrogens_().
◆ set_xyz()
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virtual |
Reimplemented in core::conformation::symmetry::SymmetricConformation.
References atom_tree_, residues_, and set_xyz_moved().
Referenced by core::conformation::carbohydrates::align_virtual_atoms_in_carbohydrate_residue(), align_virtual_atoms_in_carbohydrate_residue(), protocols::carbohydrates::IdealizeAnomericHydrogens::apply(), fill_missing_atoms(), protocols::rna::movers::RNAIdealizeMover::perturb_pose(), protocols::cyclic_peptide::PeptideStubMover::rebuild_atoms(), rebuild_polymer_bond_dependent_atoms(), rebuild_residue_connection_dependent_atoms(), core::conformation::symmetry::recenter(), core::io::pose_from_sfr::PoseFromSFRBuilder::refine_pose(), protocols::fibril::reorient_extended_fibril(), core::conformation::symmetry::SymmetricConformation::set_xyz(), and core::conformation::update_cutpoint_virtual_atoms_if_connected().
◆ set_xyz_moved() [1/2]
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inlineprivate |
notify of xyz-change
References residue_torsions_need_updating_, structure_moved_, and xyz_moved_.
Referenced by batch_set_xyz(), and set_xyz().
◆ set_xyz_moved() [2/2]
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inlineprivate |
notify of mutiple-xyz-change
References residue_torsions_need_updating_, structure_moved_, and xyz_moved_.
◆ setup_atom_tree()
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private |
(re-)builds the AtomTree using the FoldTree and the Residues
References atom_tree_, core::conformation::build_tree(), const_residues(), fold_tree_, residue_coordinates_need_updating_, residue_torsions_need_updating_, and update_residue_torsions().
Referenced by append_residue(), append_residues(), delete_residue_range_slow(), delete_residue_slow(), fold_tree(), and insert_conformation_by_jump().
◆ setup_glycan_trees()
| void core::conformation::Conformation::setup_glycan_trees | ( | ) |
Setup glycan trees and attach length observer.
References core::conformation::TR(), and tree_set_observer_.
Referenced by core::pose::symmetry::extract_asymmetric_unit(), core::pose::symmetry::get_asymmetric_pose_copy_from_symmetric_pose(), core::pose::carbohydrates::glycosylate_pose(), insert_conformation_by_jump(), core::pose::symmetry::make_asymmetric_pose(), core::pose::make_pose_from_saccharide_sequence(), core::pose::symmetry::make_symmetric_pose(), and core::io::pose_from_sfr::PoseFromSFRBuilder::refine_pose().
◆ sever_chemical_bond()
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virtual |
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).
References core::conformation::Residue::mark_connect_incomplete(), and residue_().
Referenced by protocols::metal_interface::RemoveMetalConnectionsMover::apply(), core::pose::correctly_add_2prime_connection_variants(), core::pose::declare_cutpoint_chemical_bond(), core::pose::fix_up_residue_type_variants_at_strand_beginning(), and core::pose::fix_up_residue_type_variants_at_strand_end().
◆ show_residue_connections() [1/2]
| void core::conformation::Conformation::show_residue_connections | ( | ) | const |
Show residue connections for debugging purposes.
References core::conformation::TR().
Referenced by core::conformation::operator<<().
◆ show_residue_connections() [2/2]
| void core::conformation::Conformation::show_residue_connections | ( | std::ostream & | os | ) | const |
Show residue connections for debugging purposes.
- Note
- This method is a rewrite of an earlier version to include an argument for desired output stream. This is to be more consistent with typical show() methods and allows for simple << operator overloading for use in PyRosetta. ~ Labonte
References core::conformation::Residue::connect_map(), core::chemical::ResConnID::connid(), core::conformation::Residue::n_non_polymeric_residue_connections(), core::conformation::Residue::n_polymeric_residue_connections(), core::conformation::Residue::n_possible_residue_connections(), core::conformation::Residue::name(), core::chemical::ResConnID::resid(), core::conformation::Residue::residue_connect_atom_index(), residues_, and size().
◆ size()
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inline |
Returns the number of residues in the Conformation.
References residues_.
Referenced by aa(), add_disulfide_bond(), protocols::denovo_design::components::add_to_pose(), protocols::environment::EnvClaimBroker::add_virtual_residues(), core::conformation::annotated_atom_graph_from_conformation(), annotated_sequence(), append_polymer_residue_after_seqpos(), append_residue(), append_residue_by_bond(), append_residue_by_jump(), append_residues(), apply_transform_Rx_plus_v(), core::conformation::symmetry::SymmetricConformation::apply_transform_Rx_plus_v(), core::conformation::atom_graph_from_conformation(), core::chemical::ICoorAtomID::atom_id(), protocols::idealize::basic_idealize(), core::conformation::break_disulfide(), protocols::environment::EnvClaimBroker::broker_fold_tree(), chain_end(), chain_endings(), chains_from_termini(), protocols::environment::collect_dofs(), Conformation(), const_residue_(), const_residues(), copy_segment(), debug_residue_torsions(), delete_polymer_residue(), delete_residue_range_slow(), delete_residue_slow(), detect_bonds(), detect_disulfides(), core::conformation::symmetry::SymmetricConformation::detect_disulfides(), detect_pseudobonds(), core::conformation::disulfide_bonds(), protocols::viewer::dump_residue_kinemage(), protocols::viewer::dump_structure_kinemage(), core::energy_methods::FullatomDisulfideEnergy::ensure_lrenergy_container_is_up_to_date(), fill_missing_atoms(), protocols::environment::find_implied_cut(), protocols::simple_moves::asym_fold_and_dock::AsymFoldandDockMoveRbJumpMover::find_new_jump_residue(), core::pose::symmetry::find_new_symmetric_jump_residues(), fold_tree(), core::conformation::get_disulf_partner(), core::conformation::carbohydrates::get_glycan_start_points(), core::conformation::idealize_position(), in_place_copy(), core::pose::initialize_atomid_map(), core::pose::initialize_atomid_map_heavy_only(), insert_chain_ending(), insert_conformation_by_jump(), core::conformation::symmetry::MirrorSymmetricConformation::insert_conformation_by_jump(), core::conformation::symmetry::SymmetricConformation::insert_conformation_by_jump(), core::conformation::insert_ideal_bonds_at_polymer_junction(), core::conformation::insert_ideal_mainchain_bonds(), insert_polymer_residue(), insert_residue_by_bond(), insert_residue_by_jump(), core::conformation::Residue::inter_residue_connection_partner(), core::conformation::is_ideal_position(), core::conformation::signals::LengthEvent::LengthEvent(), operator=(), core::conformation::Residue::orient_onto_residue_peptoid(), prepend_polymer_residue_before_seqpos(), core::conformation::symmetry::process_residue_request(), core::conformation::membrane::membrane_geometry::Bicelle::protein_slice_diameter_at_mem_cen(), core::scoring::bin_transitions::BinTransitionCalculator::random_bin_based_on_prev_and_next(), core::conformation::symmetry::SymmetricConformation::recalculate_transforms(), core::conformation::symmetry::recenter(), rederive_chain_endings(), rederive_chain_ids(), protocols::fibril::reorient_extended_fibril(), residue(), residue_(), residue_cop(), residue_data(), core::conformation::residue_point_graph_from_conformation(), residue_type(), residue_type_ptr(), residue_typeset_mode(), protocols::hybridization::DomainAssembly::run(), sequence_matches(), core::conformation::symmetry::set_fold_tree_from_symm_data(), core::conformation::carbohydrates::GlycanTreeSet::setup_glycan_trees(), core::conformation::symmetry::setup_symmetric_conformation(), show_residue_connections(), protocols::environment::Environment::start(), core::conformation::symmetry::symmetrize_fold_tree(), update_actcoords(), update_domain_map(), update_noncanonical_connection(), core::conformation::symmetry::SymmetricConformation::update_noncanonical_connection(), update_polymeric_connection(), core::conformation::parametric::ParametersSet::update_residue_links(), update_residue_torsions(), update_sequence_numbering(), and core::conformation::ConformationKinWriter::write_coords().
◆ structure_moved()
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inline |
has the structure moved since the last call to reset_move_data or reset_structure_moved
References structure_moved_.
Referenced by core::pack::create_packer_graph(), protocols::features::AtomAtomPairFeatures::report_atom_pairs(), protocols::features::AtomInResidueAtomInResiduePairFeatures::report_atom_pairs(), protocols::features::HBondFeatures::report_features(), protocols::features::TaskOperationFeatures::report_features(), and protocols::features::PairFeatures::report_residue_pairs().
◆ stub_from_id()
| kinematics::Stub core::conformation::Conformation::stub_from_id | ( | id::StubID const & | id | ) | const |
◆ torsion()
Return the torsion angle OR rigid-body offset for <id>
- Remarks
- This is a poorly named method, as it can also be used to access jump rigid-body offsets. ~Labonte
References atom_tree_, core::id::BB, core::id::BRANCH, core::conformation::Res