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Rosetta
2020.11
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Rosetta
2020.11
|
A symmetric conformation: has an additional data member "SymmetryInfo" class. More...
#include <SymmetricConformation.hh>
Public Member Functions | |
| SymmetricConformation () | |
| Default CTOR. More... | |
| SymmetricConformation (Conformation const &conf, SymmetryInfo const &symm_info) | |
| Default CTOR. More... | |
| Conformation & | operator= (Conformation const &src) override |
| copy constructor More... | |
| void | detached_copy (Conformation const &src) override |
| 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... | |
| ConformationOP | clone () const override |
| bool | same_type_as_me (Conformation const &other, bool const recurse=true) const override |
| determine the type of the ConformationOP More... | |
| virtual SymmetryInfoCOP | Symmetry_Info () const |
| virtual SymmetryInfoOP | Symmetry_Info () |
| void | set_dof (DOF_ID const &id, Real const setting) override |
| DOF. More... | |
| void | set_secstruct (Size const seqpos, char const setting) override |
| set the secondary structure of a sequence position More... | |
| void | set_torsion (TorsionID const &id, Real const setting) override |
| BONDS/TORSIONS. More... | |
| void | set_jump (int const jump_number, Jump const &new_jump) override |
| set a jump More... | |
| void | set_jump (AtomID const &id, Jump const &new_jump) override |
| set a jump More... | |
| void | set_bond_angle (AtomID const &atom1, AtomID const &atom2, AtomID const &atom3, Real const setting) override |
| BOND ANGLES. More... | |
| void | set_bond_length (AtomID const &atom1, AtomID const &atom2, Real const setting) override |
| BOND LENGTHS. More... | |
| void | set_torsion_angle (AtomID const &atom1, AtomID const &atom2, AtomID const &atom3, AtomID const &atom4, Real const setting, bool const quiet=false) override |
| TORSION ANGLES. More... | |
| utility::vector1< bool > | get_residue_mask () const override |
| Real | get_residue_weight (core::Size resid1, core::Size resid2) const override |
| returns a residue-pair weight More... | |
| void | replace_residue (Size const seqpos, Residue const &new_rsd, bool const orient_backbone) override |
| replace residue More... | |
| void | replace_residue (Size const seqpos, Residue const &new_rsd, utility::vector1< std::pair< std::string, std::string > > const &atom_pairs) override |
| void | fold_tree (FoldTree const &fold_tree_in) override |
| set the fold_tree .. update symminfo if jump numbering changed More... | |
| FoldTree const & | fold_tree () const override |
| FoldTree access. More... | |
| numeric::HomogeneousTransform < core::Real > | get_transformation (core::Size resid) |
| Get the transformation controlling resid i. More... | |
| virtual PointPosition | apply_transformation (PointPosition Xin, core::Size residfrom, core::Size residto, bool rotationonly=false) |
| Remap coordinate X from resid i's frame to resid j's frame. More... | |
| virtual PointPosition | apply_transformation_norecompute (PointPosition Xin, core::Size residfrom, core::Size residto, bool rotationonly=false) const |
| Remap coordinate X from resid i's frame to resid j's frame assumes that the transformations are already computed (thus can be const) More... | |
| virtual void | recalculate_transforms () |
| void | set_xyz (AtomID const &id, PointPosition const &position) override |
| Symmetric set_xyz. More... | |
| void | batch_set_xyz (utility::vector1< AtomID > const &ids, utility::vector1< PointPosition > const &positions) override |
| Symmetric batch_set_xyz. More... | |
| void | apply_transform_Rx_plus_v (numeric::xyzMatrix< Real > const &R, Vector const &v) override |
| ~SymmetricConformation () override | |
| 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) override |
| Append a new residue by a jump; clones this append to all copies. More... | |
| void | append_polymer_residue_after_seqpos (conformation::Residue const &new_rsd, Size const seqpos, bool const build_ideal_geometry=true) override |
| Apped a new residue after a given position in the pose. More... | |
| void | safely_append_polymer_residue_after_seqpos (conformation::Residue const &new_rsd, Size const seqpos, bool const build_ideal_geometry=true) override |
| glues to seqpos and perhaps also seqpos+1, removes termini variants if necessary More... | |
| void | prepend_polymer_residue_before_seqpos (conformation::Residue const &new_rsd, Size const seqpos, bool const build_ideal_geometry=true) override |
| Prepend a new residue after a given position in the pose. More... | |
| void | safely_prepend_polymer_residue_before_seqpos (conformation::Residue const &new_rsd, Size const seqpos, bool const build_ideal_geometry=true) override |
| glues to seqpos and perhaps also seqpos-1, removes termini variants if necessary More... | |
| 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="") override |
| Append a new conformation by a jump; clones this append to all copies. More... | |
| void | detect_disulfides (utility::vector1< Size > const &disulf_one=utility::vector1< core::Size >(), utility::vector1< Size > const &disulf_two=utility::vector1< core::Size >()) override |
| Detect existing disulfides from the protein structure. More... | |
| void | declare_chemical_bond (Size const seqpos1, std::string const &atom_name1, Size const seqpos2, std::string const &atom_name2) override |
| Declare that a chemical bond exists between two residues. More... | |
| void | update_noncanonical_connection (Size lower_seqpos, Size lr_conn_id, Size upper_seqpos, Size ur_conn_id) override |
| 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, in addition to ALL clones. More... | |
 Public Member Functions inherited from core::conformation::Conformation | |
| iterator | begin () noexcept |
| const_iterator | begin () const noexcept |
| iterator | end () noexcept |
| const_iterator | end () const noexcept |
| Conformation () | |
| constructor More... | |
| ~Conformation () override | |
| default destructor More... | |
| Conformation (Conformation const &src) | |
| copy constructor More... | |
| void | clear () |
| clear data More... | |
| ConformationCOP | get_self_ptr () const |
| self pointers More... | |
| ConformationOP | get_self_ptr () |
| ConformationCAP | get_self_weak_ptr () const |
| ConformationAP | get_self_weak_ptr () |
| void | debug_residue_torsions (bool verbose=false) const |
| debugging More... | |
| void | show_residue_connections () const |
| Show residue connections for debugging purposes. More... | |
| void | show_residue_connections (std::ostream &os) const |
| Show residue connections for debugging purposes. More... | |
| bool | sequence_matches (Conformation const &other) const |
| do the names of all residues in this and src match? More... | |
| Size | size () const |
| Returns the number of residues in the Conformation. More... | |
| bool | empty () const |
| Returns true if this conformation does not have any residues. More... | |
| core::chemical::ResidueTypeSetCOP | residue_type_set_for_conf (core::chemical::TypeSetMode mode=core::chemical::INVALID_t) const |
| Return the appropriate ResidueTypeSet for the Conformation If mode is INVALID_t (the default), then return the typeset for the majority mode of the Conformation. Note: This may be a GlobalResidueTypeSet, if the Conformation doesn't have a specific PoseResidueTypeSet. More... | |
| core::chemical::PoseResidueTypeSetOP | modifiable_residue_type_set_for_conf (core::chemical::TypeSetMode mode=core::chemical::INVALID_t) const |
| Return a clone of the Conformation-specific PoseResidueTypeSet (note this is const) Modifications to this RTS won't be seen in the Conformation unless you pass it back in with reset_residue_type_set_for_conf() Should always return a non-null pointer: will create a new PoseResidueTypeSet if the Conformation doesn't have it already. More... | |
| void | reset_residue_type_set_for_conf (core::chemical::PoseResidueTypeSetCOP new_set, core::chemical::TypeSetMode mode=core::chemical::INVALID_t) |
| Reset the Conformation-specific PoseResidueTypeSet for the appropriate mode to the given RTS. (If the given mode is INVALID_t (the recommended default) the mode will be auto-determined from the RTS.) More... | |
| core::chemical::TypeSetMode | residue_typeset_mode (bool majority=true) const |
| What mode of ResidueTypeSet is this Conformation made of? If majority is true, it will be the mode of the ResidueTypes for most residues in the pose. If majority is false, core::chemical::MIXED_t will be returned for conformations with ResidueTypes of multiple modes. More... | |
| bool | is_fullatom () const |
| convenience test for residue_type_set mode More... | |
| bool | is_centroid () const |
| convenience test for residue_type_set mode More... | |
| bool | is_mixed_mode () const |
| convenience test for residue_type_set mode More... | |
| bool | is_membrane () const |
| convenience test for if the conformation contains information for a membrane protein More... | |
| bool | contains_carbohydrate_residues () const |
| Return true if this conformation contains any carbohydrate residues. More... | |
| void | contains_carbohydrate_residues (bool setting) |
| Set whether this conformation contains any carbohydrate residues. More... | |
| Size | chain_end (Size chain) const |
| Returns the position number of the last residue in chain number <chain> More... | |
| Size | chain_begin (Size chain) const |
| Returns the position number of the first residue in chain number <chain> More... | |
| Size | num_chains () const |
| Returns the number of chains. More... | |
| utility::vector1< Size > const & | chain_endings () const |
| Returns the list of (chain number) chain endings. More... | |
| 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... | |
| 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... | |
| AtomTree const & | atom_tree () const |
| Returns the conformation's AtomTree. More... | |
| chemical::AA const & | aa (Size seqpos) const |
| Returns the AA enum for position <seqpos> More... | |
| std::string | annotated_sequence (bool show_all_variants) const |
| Returns the variant-tagged string representing the residue types that make up a conformation; e.g. M[MET:N-Terminus-Variant]CDH[HIS_D]LLR[ARG:C-Terminus-Variant]. More... | |
| Residue const & | residue (Size seqpos) const |
| access one of the residues More... | |
| basic::datacache::BasicDataCache const & | residue_data (Size seqpos) const |
| Read access to the datacache array stored inside a Residue object. Also accessible to the user by calling residue( seqpos ).data_ptr() directly. More... | |
| basic::datacache::BasicDataCache & | residue_data (Size seqpos) |
| Write access to the datacache array stored inside a Residue object. Although the Conformation very deliberately does not grant users write access to the whole of its Residue objects, it will grant users access to the Residue objects data cache. So while the coordinates and dihedrals of the Residue will not be changable e.g. during the setup-for-scoring phase, data derived from those coordinates and dihedrals and which ends up living in the Residue will be changable. More... | |
| ResidueCOP | residue_cop (Size seqpos) const |
| access one of the residues, using COP More... | |
| chemical::ResidueType const & | residue_type (Size seqpos) const |
| access one of the residue's types – avoids coord/torsion update More... | |
| chemical::ResidueTypeCOP | residue_type_ptr (Size seqpos) const |
| access one of the residue's types as a COP – avoids coord/torsion update More... | |
| ResidueCOPs | const_residues () const |
| Inefficient – constructs copy of residues_. More... | |
| void | insert_residue_by_jump (Residue const &new_rsd_in, Size seqpos, Size anchor_pos, std::string const &anchor_atom="", std::string const &root_atom="", bool new_chain=false) |
| Insert a new residue by jump. If new_chain is "true", then seqpos must be the last residue of one chain (i.e. residue(seqpos).chain() != residue(seqpos+1).chain() ) More... | |
| void | insert_residue_by_bond (Residue const &new_rsd_in, Size const seqpos, Size anchor_pos, bool const build_ideal_geometry=false, std::string const &anchor_atom="", std::string const &root_atom="", bool new_chain=false, bool const lookup_bond_length=false) |
| Insert a new residue by jump. If new_chain is "true", then seqpos must be the last residue of one chain (i.e. residue(seqpos).chain() != residue(seqpos+1).chain() ) More... | |
| void | append_residue_by_bond (conformation::Residue const &new_rsd, bool const build_ideal_geometry=false, int connection_index=0, Size anchor_residue=0, int anchor_connection_index=0, bool const start_new_chain=false, bool const lookup_bond_length=false) |
| Append a new residue by a bond. More... | |
| virtual 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... | |
| void | detect_bonds () |
| void | detect_pseudobonds () |
| virtual void | sever_chemical_bond (Size seqpos1, Size res1_resconn_index, Size seqpos2, Size res2_resconn_index) |
| Sever the chemical bond between two residues by stating that the connections for those residues are "incomplete" (i.e. in a state where these residues are not ready to be scored). More... | |
| void | rebuild_polymer_bond_dependent_atoms_this_residue_only (Size const seqpos) |
| Rebuilds the atoms that are dependent on polymer bonds for the specified residue only. More... | |
| 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... | |
| 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 | fix_disulfides (utility::vector1< std::pair< Size, Size > > const &disulf_bonds) |
| Assigns disulfide bonds based on a pre-determined list. More... | |
| void | create_new_parameters_set () |
| Create a new (empty) ParametersSet object and add its owning pointer to the current Conformation object. More... | |
| void | add_parameters_set (ParametersSetOP newset) |
| Add a (predefined) ParametersSet object (via its owning pointer) to the current Conformation object. More... | |
| core::Size | n_parameters_sets () const |
| Get the number of parameters sets defined for this Conformation. More... | |
| void | clear_parameters_set_list () |
| Delete the list of ParametersSetOP objects. More... | |
| ParametersSetOP | parameters_set (core::Size const index) |
| Access one of the ParametersSets objects linked to this Conformation. More... | |
| ParametersSetCOP | parameters_set (core::Size const index) const |
| Const access to one of the ParametersSets objects linked to this Conformation. More... | |
| void | copy_segment (Size size, Conformation const &src, Size begin, Size src_begin) |
| copy a stretch of coordinates/torsions from another Conformation More... | |
| 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... | |
| Real | torsion (TorsionID const &id) const |
| Return the torsion angle OR rigid-body offset for <id> More... | |
| Real | torsion_angle (AtomID const &atom1, AtomID const &atom2, AtomID const &atom3, AtomID const &atom4) const |
| Returns the torsion angle defined by <atom[1-4]> in Radians. More... | |
| Real | bond_angle (AtomID const &atom1, AtomID const &atom2, AtomID const &atom3) const |
| Returns the bond angle defined by <atom[1-3]> through the AtomTree. More... | |
| Real | bond_length (AtomID const &atom1, AtomID const &atom2) const |
| Returns the bond length between <atom1> and <atom2> through the AtomTree. More... | |
| core::Vector | bond_orientation (AtomID const &atom1, AtomID const &atom2) const |
| Return the normalized vector of the bond between these two atoms. More... | |
| core::Vector | bond_orientation (core::id::TorsionID const torsion) const |
| Return the normalized vector of the bond about which this torsion angle twists. More... | |
| const Jump & | jump (int jump_number) const |
| Returns the Jump with jump number <jump_number> More... | |
| const Jump & | jump (AtomID const &id) const |
| access a jump More... | |
| PointPosition const & | xyz (AtomID const &id) const |
| access xyz coordinates of an atom More... | |
| virtual void | batch_get_xyz (utility::vector1< AtomID > const &id, utility::vector1< PointPosition > &position) const |
| virtual void | insert_ideal_geometry_at_polymer_bond (Size const seqpos) |
| virtual void | insert_ideal_geometry_at_residue_connection (Size const pos1, Size const connid1) |
| 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 | |
| void | clear_Tsymm () |
| void | invert_Tsymm (char sub, core::Size subunit) |
| core::Size | get_upstream_vrt (core::Size seqpos) const |
| Protected Member Functions inherited from core::conformation::Conformation | |
| Residue const & | const_residue_ (Size seqpos) const |
| Returns a constant residue reference without triggering coordinate/torsion update. More... | |
| void | force_update_residue_torsions () const |
| Force updating of residue torsions. More... | |
| void | force_update_residue_coordinates () const |
| Force updating of residue coordinates. More... | |
Private Attributes | |
| SymmetryInfoOP | symm_info_ |
| std::map< char, utility::vector1 < SymmetryTransform > > | Tsymm_ |
A symmetric conformation: has an additional data member "SymmetryInfo" class.
Handles symmetrizing of some of the conformation-changing methods of Conformation
| core::conformation::symmetry::SymmetricConformation::SymmetricConformation | ( | ) |
| core::conformation::symmetry::SymmetricConformation::SymmetricConformation | ( | Conformation const & | conf, |
| SymmetryInfo const & | symm_info | ||
| ) |
Default CTOR.
References clear_Tsymm(), core::conformation::symmetry::SymmetryInfo::clone(), and symm_info_.
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References core::conformation::Conformation::clear().
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Apped a new residue after a given position in the pose.
Reimplemented from core::conformation::Conformation.
References core::conformation::Conformation::append_polymer_residue_after_seqpos(), apply_transformation(), fold_tree(), core::conformation::symmetry::get_asymm_unit_fold_tree(), core::conformation::Residue::natoms(), core::conformation::Residue::set_xyz(), symm_info_, core::conformation::symmetry::symmetrize_fold_tree(), and core::conformation::Residue::xyz().
Referenced by safely_append_polymer_residue_after_seqpos().
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Append a new residue by a jump; clones this append to all copies.
Reimplemented from core::conformation::Conformation.
References apply_transformation(), fold_tree(), core::conformation::symmetry::get_asymm_unit_fold_tree(), core::conformation::Conformation::insert_residue_by_jump(), core::conformation::Residue::natoms(), core::conformation::Residue::set_xyz(), symm_info_, core::conformation::symmetry::symmetrize_fold_tree(), core::conformation::symmetry::TR(), and core::conformation::Residue::xyz().
Referenced by core::conformation::symmetry::MirrorSymmetricConformation::append_residue_by_jump().
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Reimplemented from core::conformation::Conformation.
References core::conformation::Conformation::batch_set_xyz(), clear_Tsymm(), core::chemical::ResidueType::natoms(), core::conformation::Conformation::residue_type(), core::conformation::Conformation::size(), and core::conformation::Conformation::xyz().
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Remap coordinate X from resid i's frame to resid j's frame.
References recalculate_transforms(), symm_info_, and Tsymm_.
Referenced by append_polymer_residue_after_seqpos(), append_residue_by_jump(), batch_set_xyz(), declare_chemical_bond(), core::conformation::symmetry::MirrorSymmetricConformation::insert_conformation_by_jump(), insert_conformation_by_jump(), prepend_polymer_residue_before_seqpos(), core::conformation::symmetry::MirrorSymmetricConformation::replace_residue(), replace_residue(), and set_xyz().
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Remap coordinate X from resid i's frame to resid j's frame assumes that the transformations are already computed (thus can be const)
References symm_info_, and Tsymm_.
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Symmetric batch_set_xyz.
Reimplemented from core::conformation::Conformation.
References apply_transformation(), core::conformation::Conformation::batch_set_xyz(), core::conformation::Conformation::begin(), clear_Tsymm(), core::conformation::Conformation::end(), symm_info_, and core::conformation::symmetry::TR().
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References Tsymm_.
Referenced by apply_transform_Rx_plus_v(), batch_set_xyz(), recalculate_transforms(), core::conformation::symmetry::MirrorSymmetricConformation::replace_residue(), replace_residue(), set_bond_angle(), set_bond_length(), core::conformation::symmetry::MirrorSymmetricConformation::set_dof(), set_dof(), core::conformation::symmetry::MirrorSymmetricConformation::set_jump(), set_jump(), core::conformation::symmetry::MirrorSymmetricConformation::set_torsion(), set_torsion(), core::conformation::symmetry::MirrorSymmetricConformation::set_torsion_angle(), set_torsion_angle(), set_xyz(), SymmetricConformation(), and core::conformation::symmetry::MirrorSymmetricConformation::synch_mirror_jumps_with_atomtree().
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make a copy of this conformation( allocate actual memory for it )
Reimplemented from core::conformation::Conformation.
References symm_info_, and SymmetricConformation().
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Declare that a chemical bond exists between two residues.
This updates all symmetry copies, so that each one has a chemical bond between the residues in question.
This updates all symmetry copies, so that each one has a chemical bond between the residues in question.
Reimplemented from core::conformation::Conformation.
References apply_transformation(), core::conformation::Conformation::declare_chemical_bond(), core::conformation::Conformation::residue(), symm_info_, core::conformation::symmetry::TR(), and core::conformation::Conformation::xyz().
Referenced by detect_disulfides().
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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 from core::conformation::Conformation.
References core::conformation::Conformation::detached_copy(), symm_info_, and Tsymm_.
Referenced by core::conformation::symmetry::MirrorSymmetricConformation::detached_copy().
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Detect existing disulfides from the protein structure.
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.
Reimplemented from core::conformation::Conformation.
References core::conformation::Residue::atom(), core::conformation::Residue::atom_index(), core::chemical::ResidueType::atom_index(), core::conformation::Residue::atom_name(), core::conformation::Residue::atoms(), core::conformation::change_cys_state(), core::conformation::Conformation::const_residue_(), declare_chemical_bond(), 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::chemical::ResidueTypeBase::name(), core::chemical::ResidueTypeBase::name3(), core::conformation::Residue::nbr_atom(), core::conformation::Residue::nbr_radius(), core::conformation::Conformation::residue(), core::conformation::Conformation::residue_type(), core::conformation::Conformation::size(), symm_info_, core::conformation::symmetry::TR(), core::conformation::Residue::type(), and core::conformation::Atom::xyz().
Referenced by core::conformation::symmetry::MirrorSymmetricConformation::detect_disulfides().
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set the fold_tree .. update symminfo if jump numbering changed
set the fold_tree, update symmetryinfo
Reimplemented from core::conformation::Conformation.
References core::conformation::Conformation::fold_tree(), core::conformation::symmetry::get_asymm_unit_fold_tree(), core::kinematics::FoldTree::num_jump(), and symm_info_.
Referenced by core::conformation::symmetry::show_foldtree().
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FoldTree access.
Reimplemented from core::conformation::Conformation.
References core::conformation::Conformation::fold_tree().
Referenced by append_polymer_residue_after_seqpos(), append_residue_by_jump(), core::conformation::symmetry::MirrorSymmetricConformation::fold_tree(), get_upstream_vrt(), core::conformation::symmetry::MirrorSymmetricConformation::insert_conformation_by_jump(), insert_conformation_by_jump(), prepend_polymer_residue_before_seqpos(), recalculate_transforms(), set_dof(), and set_jump().
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Returns a mask of residues over which scoring is restricted. Only these residues will be used in constructing the neighbor list
Reimplemented from core::conformation::Conformation.
References symm_info_.
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returns a residue-pair weight
Returns a weight to be used when scoring this residue.
Reimplemented from core::conformation::Conformation.
References symm_info_.
| numeric::HomogeneousTransform< core::Real > core::conformation::symmetry::SymmetricConformation::get_transformation | ( | core::Size | resid | ) |
Get the transformation controlling resid i.
References recalculate_transforms(), symm_info_, and Tsymm_.
Referenced by core::scoring::nmr::apply_tensor_transformation(), core::scoring::nmr::apply_vector_rotation(), and core::scoring::nmr::apply_vector_transformation().
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Append a new conformation by a jump; clones this append to all copies.
Reimplemented from core::conformation::Conformation.
References apply_transformation(), core::conformation::Conformation::clone(), fold_tree(), core::conformation::Conformation::fold_tree(), core::conformation::symmetry::get_asymm_unit_fold_tree(), core::conformation::Conformation::insert_conformation_by_jump(), core::kinematics::FoldTree::num_jump(), core::conformation::Conformation::residue(), core::conformation::Conformation::size(), symm_info_, core::conformation::symmetry::symmetrize_fold_tree(), core::conformation::symmetry::TR(), and core::conformation::Residue::xyz().
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References Tsymm_.
Referenced by core::conformation::symmetry::MirrorSymmetricConformation::recalculate_transforms().
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Prepend a new residue after a given position in the pose.
Reimplemented from core::conformation::Conformation.
References apply_transformation(), core::conformation::Residue::clone(), core::conformation::Conformation::const_residue_(), fold_tree(), core::conformation::symmetry::get_asymm_unit_fold_tree(), core::conformation::Residue::is_lower_terminus(), core::conformation::Residue::lower_connect(), core::conformation::orient_residue_for_ideal_bond(), core::conformation::Conformation::prepend_polymer_residue_before_seqpos(), core::conformation::Conformation::rebuild_polymer_bond_dependent_atoms(), symm_info_, core::conformation::symmetry::symmetrize_fold_tree(), and core::conformation::Residue::xyz().
Referenced by safely_prepend_polymer_residue_before_seqpos().
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Reimplemented in core::conformation::symmetry::MirrorSymmetricConformation.
References core::conformation::Conformation::aa(), core::chemical::aa_vrt, core::conformation::Residue::atom(), clear_Tsymm(), core::conformation::ResidueFactory::create_residue(), core::kinematics::FoldTree::downstream_jump_residue(), fold_tree(), core::conformation::Residue::is_protein(), core::kinematics::FoldTree::num_jump(), core::conformation::Conformation::residue(), core::conformation::Conformation::size(), symm_info_, core::id::to_string(), Tsymm_, core::kinematics::FoldTree::upstream_jump_residue(), core::conformation::virtual_type_for_conf(), protocols::comparative_modeling::features::X, core::conformation::Atom::xyz(), core::conformation::Residue::xyz(), and core::chemical::element::Y.
Referenced by apply_transformation(), get_transformation(), core::conformation::symmetry::MirrorSymmetricConformation::recalculate_transforms(), core::scoring::methods::SmoothEnvEnergy::setup_for_derivatives(), and core::scoring::methods::RG_Energy_Fast::setup_for_derivatives().
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replace residue
symmetry-safe replace residue
Reimplemented from core::conformation::Conformation.
References apply_transformation(), clear_Tsymm(), core::conformation::Residue::natoms(), core::conformation::Conformation::replace_residue(), core::conformation::Residue::set_xyz(), symm_info_, core::conformation::symmetry::TR(), and core::conformation::Residue::xyz().
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symmetry-safe replace residue
Reimplemented from core::conformation::Conformation.
References apply_transformation(), clear_Tsymm(), core::conformation::Residue::natoms(), core::conformation::Conformation::replace_residue(), core::conformation::Residue::set_xyz(), symm_info_, core::conformation::symmetry::TR(), and core::conformation::Residue::xyz().
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glues to seqpos and perhaps also seqpos+1, removes termini variants if necessary
Reimplemented from core::conformation::Conformation.
References append_polymer_residue_after_seqpos(), core::conformation::remove_upper_terminus_type_from_conformation_residue(), and symm_info_.
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glues to seqpos and perhaps also seqpos-1, removes termini variants if necessary
Fires a LengthEvent::RESIDUE_PREPEND signal.
Reimplemented from core::conformation::Conformation.
References prepend_polymer_residue_before_seqpos(), core::conformation::remove_lower_terminus_type_from_conformation_residue(), and symm_info_.
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determine the type of the ConformationOP
Reimplemented from core::conformation::Conformation.
References core::conformation::Conformation::same_type_as_me().
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BOND ANGLES.
Reimplemented from core::conformation::Conformation.
References core::id::AtomID::atomno(), clear_Tsymm(), core::id::AtomID::rsd(), core::conformation::Conformation::set_bond_angle(), symm_info_, and core::conformation::symmetry::TR().
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BOND LENGTHS.
Reimplemented from core::conformation::Conformation.
References core::id::AtomID::atomno(), clear_Tsymm(), core::id::AtomID::rsd(), core::conformation::Conformation::set_bond_length(), symm_info_, and core::conformation::symmetry::TR().
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DOF.
Reimplemented from core::conformation::Conformation.
References clear_Tsymm(), core::conformation::Conformation::dof(), core::kinematics::FoldTree::downstream_jump_residue(), fold_tree(), core::id::RB1, core::id::RB6, core::conformation::Conformation::set_dof(), symm_info_, and core::conformation::symmetry::TR().
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set a jump
JUMPS.
JUMPS
Reimplemented from core::conformation::Conformation.
References clear_Tsymm(), core::conformation::Conformation::jump_atom_id(), core::conformation::Conformation::set_jump(), symm_info_, and core::conformation::symmetry::TR().
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set a jump
Reimplemented from core::conformation::Conformation.
References clear_Tsymm(), fold_tree(), core::conformation::Conformation::jump_atom_id(), core::conformation::Conformation::set_jump(), symm_info_, and core::conformation::symmetry::TR().
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set the secondary structure of a sequence position
Sets secondary structure character of a sequence position. Will resize the secondary structure array if the requested sequence position is larger than the length of the array.
Reimplemented from core::conformation::Conformation.
References core::conformation::Conformation::set_secstruct(), symm_info_, and core::conformation::symmetry::TR().
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BONDS/TORSIONS.
TORSIONS.
Reimplemented from core::conformation::Conformation.
References clear_Tsymm(), core::conformation::Conformation::set_torsion(), symm_info_, core::conformation::Conformation::torsion(), and core::conformation::symmetry::TR().
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TORSION ANGLES.
Reimplemented from core::conformation::Conformation.
References core::id::AtomID::atomno(), clear_Tsymm(), core::id::AtomID::rsd(), core::conformation::Conformation::set_torsion_angle(), symm_info_, and core::conformation::symmetry::TR().
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Symmetric set_xyz.
Reimplemented from core::conformation::Conformation.
References apply_transformation(), core::conformation::Conformation::begin(), clear_Tsymm(), core::conformation::Conformation::end(), core::id::AtomID::rsd(), core::conformation::Conformation::set_xyz(), symm_info_, and core::conformation::symmetry::TR().
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References symm_info_.
Referenced by protocols::simple_filters::BuriedUnsatHbondFilter::compute(), core::scoring::methods::RG_Energy_Fast::eval_atom_derivative(), core::conformation::symmetry::get_asymm_unit_fold_tree(), core::pose::symmetry::get_nres_asymmetric_unit(), core::conformation::symmetry::MirrorSymmetricConformation::get_residue_weight(), protocols::hbnet::hbnet_symm_one_body_energies(), core::pack::hbonds::hbond_graph_from_partial_rotsets(), core::conformation::symmetry::MirrorSymmetricConformation::insert_conformation_by_jump(), protocols::hbnet::HBNetStapleInterface::network_meets_final_criteria(), core::conformation::symmetry::MirrorSymmetricConformation::recalculate_transforms(), core::conformation::symmetry::MirrorSymmetricConformation::replace_residue(), core::conformation::symmetry::MirrorSymmetricConformation::set_dof(), core::conformation::symmetry::MirrorSymmetricConformation::set_jump(), core::conformation::symmetry::MirrorSymmetricConformation::set_torsion(), core::conformation::symmetry::MirrorSymmetricConformation::set_torsion_angle(), core::conformation::symmetry::shift_jump_numbers_in_dofs(), core::conformation::symmetry::show_foldtree(), core::scoring::sym_rmsd_with_super_subset(), core::conformation::symmetry::symmetrize_fold_tree(), core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::three_body_approximate_buried_unsat_calculation(), core::conformation::symmetry::MirrorSymmetricConformation::update_njumps_nres(), and core::conformation::symmetry::MirrorSymmetricConformation::update_residue_identities().
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References symm_info_.
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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, in addition to ALL clones.
Reimplemented from core::conformation::Conformation.
References core::conformation::Conformation::residue(), core::conformation::Conformation::set_noncanonical_connection(), core::conformation::Conformation::size(), symm_info_, and core::conformation::symmetry::TR().
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Referenced by append_polymer_residue_after_seqpos(), append_residue_by_jump(), apply_transformation(), apply_transformation_norecompute(), batch_set_xyz(), clone(), declare_chemical_bond(), detached_copy(), detect_disulfides(), fold_tree(), get_residue_mask(), get_residue_weight(), get_transformation(), insert_conformation_by_jump(), prepend_polymer_residue_before_seqpos(), recalculate_transforms(), replace_residue(), safely_append_polymer_residue_after_seqpos(), safely_prepend_polymer_residue_before_seqpos(), set_bond_angle(), set_bond_length(), set_dof(), set_jump(), set_secstruct(), set_torsion(), set_torsion_angle(), set_xyz(), SymmetricConformation(), Symmetry_Info(), and update_noncanonical_connection().
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1.8.7