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Rosetta
2015.31
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Rosetta
2015.31
|
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= (SymmetricConformation const &src) |
| copy constructor More... | |
| virtual Conformation & | operator= (Conformation const &src) |
| equals operator. Must override this, since the operator= that takes a SymmetricConformation will not be used if both references are of type Conformation. More... | |
| ConformationOP | clone () const |
| virtual bool | same_type_as_me (Conformation const &other, bool recurse) const |
| determine the type of the ConformationOP More... | |
| SymmetryInfoCOP | Symmetry_Info () const |
| SymmetryInfoOP | Symmetry_Info () |
| virtual void | set_dof (DOF_ID const &id, Real setting) |
| DOF. More... | |
| void | set_secstruct (Size seqpos, char setting) |
| set the secondary structure of a sequence position More... | |
| virtual void | set_torsion (TorsionID const &id, Real setting) |
| BONDS/TORSIONS. More... | |
| virtual void | set_jump (int jump_number, Jump const &new_jump) |
| set a jump More... | |
| virtual void | set_jump (AtomID const &id, Jump const &new_jump) |
| set a jump More... | |
| virtual void | set_bond_angle (AtomID const &atom1, AtomID const &atom2, AtomID const &atom3, Real setting) |
| BOND ANGLES. More... | |
| virtual void | set_bond_length (AtomID const &atom1, AtomID const &atom2, Real setting) |
| BOND LENGTHS. More... | |
| virtual void | set_torsion_angle (AtomID const &atom1, AtomID const &atom2, AtomID const &atom3, AtomID const &atom4, Real setting, bool quiet=false) |
| TORSION ANGLES. More... | |
| virtual utility::vector1< bool > | get_residue_mask () const |
| virtual Real | get_residue_weight (core::Size resid1, core::Size resid2) const |
| returns a residue-pair weight More... | |
| virtual void | replace_residue (Size seqpos, Residue const &new_rsd, bool orient_backbone) |
| replace residue More... | |
| virtual void | replace_residue (Size seqpos, Residue const &new_rsd, utility::vector1< std::pair< std::string, std::string > > const &atom_pairs) |
| virtual void | fold_tree (FoldTree const &fold_tree_in) |
| set the fold_tree .. update symminfo if jump numbering changed More... | |
| virtual FoldTree const & | fold_tree () const |
| FoldTree access. More... | |
| numeric::HomogeneousTransform < core::Real > | get_transformation (core::Size resid) |
| Get the transformation controlling resid i. More... | |
| 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... | |
| 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... | |
| void | recalculate_transforms () |
| virtual void | set_xyz (AtomID const &id, PointPosition const &position) |
| Symmetric set_xyz. More... | |
| virtual void | batch_set_xyz (utility::vector1< AtomID > const &ids, utility::vector1< PointPosition > const &positions) |
| Symmetric batch_set_xyz. More... | |
| virtual | ~SymmetricConformation () |
| void | append_residue_by_jump (conformation::Residue const &new_rsd, Size anchor_residue, std::string const &anchor_atom="", std::string const &root_atom="", bool start_new_chain=false) |
| Append a new residue by a jump; clones this append to all copies. More... | |
| void | insert_conformation_by_jump (Conformation const &conf, Size insert_seqpos, Size insert_jumppos, Size anchor_pos, Size anchor_jump_number=0, std::string const &anchor_atom="", std::string const &root_atom="") |
| Append a new conformation by a jump; clones this append to all copies. More... | |
| virtual void | detect_disulfides () |
| Detect existing disulfides from the protein structure. More... | |
 Public Member Functions inherited from core::conformation::Conformation | |
| Conformation () | |
| constructor More... | |
| virtual | ~Conformation () |
| 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... | |
| bool | is_residue_typeset (std::string tag) const |
| convenience test for residue_type_set ( based on two middle residue – to avoid hitting on ligands or pseudos ) More... | |
| bool | is_fullatom () const |
| convenience test for residue_type_set ( based on two middle residue – to avoid hitting on ligands or pseudos ) More... | |
| bool | is_centroid () const |
| convenience test for residue_type_set ( based on two middle residue – to avoid hitting on ligands or pseudos ) 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> More... | |
| Size | chain_begin (Size chain) const |
| Returns the position number of the first residue in <chain> More... | |
| Size | num_chains () const |
| Returns the number of chains. More... | |
| utility::vector1< Size > const & | chain_endings () const |
| Returns the list of chain endings. More... | |
| void | chain_endings (utility::vector1< Size > const &endings) |
| Sets the list of chain endings. More... | |
| void | insert_chain_ending (Size seqpos) |
| Marks <seqpos> as the end of a new chain. More... | |
| void | delete_chain_ending (Size seqpos) |
| Deletes <seqpos> from the list of chain endings. More... | |
| void | reset_chain_endings () |
| Resets chain data so that the Conformation is marked as a single chain. More... | |
| void | chains_from_termini () |
| Rederive the 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... | |
| 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... | |
| Residue const & | residue (Size seqpos) const |
| access one of the residues More... | |
| ResidueOP | residue_op (Size seqpos) |
| Access one of the residues, using OP. 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... | |
| 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 seqpos, Size anchor_pos, bool build_ideal_geometry=false, std::string const &anchor_atom="", std::string const &root_atom="", bool new_chain=false, bool lookup_bond_length=false) |
| Insert a new residue by jump. If new_chain is "true", then seqpos must be the last. More... | |
| void | append_residue_by_bond (conformation::Residue const &new_rsd, bool build_ideal_geometry=false, int connection_index=0, Size anchor_residue=0, int anchor_connection_index=0, bool start_new_chain=false, bool lookup_bond_length=false) |
| Append a new residue by a bond. More... | |
| void | append_polymer_residue_after_seqpos (Residue const &new_rsd, Size seqpos, bool build_ideal_geometry) |
| glues to seqpos and perhaps also seqpos+1 More... | |
| void | safely_append_polymer_residue_after_seqpos (Residue const &new_rsd, Size seqpos, bool build_ideal_geometry) |
| glues to seqpos and perhaps also seqpos+1, removes termini variants if necessary More... | |
| void | prepend_polymer_residue_before_seqpos (Residue const &new_rsd, Size seqpos, bool build_ideal_geometry) |
| glues to seqpos and perhaps also seqpos-1 More... | |
| void | safely_prepend_polymer_residue_before_seqpos (Residue const &new_rsd, Size seqpos, bool build_ideal_geometry) |
| glues to seqpos and perhaps also seqpos-1, removes termini variants if necessary More... | |
| virtual void | replace_residue (Size 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... | |
| void | delete_polymer_residue (Size seqpos) |
| Delete polymer residue at the given sequence position. More... | |
| void | delete_residue_slow (Size seqpos) |
| Slow method that relies on FoldTree::delete_seqpos, rebuilds atomtree, can handle jumps/root residue. More... | |
| void | delete_residue_range_slow (Size range_begin, Size range_end) |
| Slow method that relies on FoldTree::delete_seqpos, rebuilds atomtree, can handle jumps/root residue. More... | |
| void | detect_bonds () |
| void | detect_pseudobonds () |
| void | declare_chemical_bond (Size seqpos1, std::string const &atom_name1, Size 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 seqpos) |
| Rebuilds the atoms that are depenent on polymer bonds for the specified residue only. More... | |
| void | rebuild_polymer_bond_dependent_atoms (Size 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... | |
| utility::vector1 < core::id::AtomID > | bonded_neighbor_all_res (core::id::AtomID atomid, bool virt=false) const |
| get all atoms bonded to another More... | |
| 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... | |
| 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... | |
| 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... | |
| 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... | |
| void | fix_disulfides (utility::vector1< std::pair< Size, Size > > disulf_bonds) |
| Assigns disulfide bonds based on a pre-determined list. More... | |
| virtual void | create_new_parameters_set () |
| Create a new (empty) ParametersSet object and add its owning pointer to the current Conformation object. More... | |
| virtual void | add_parameters_set (ParametersSetOP newset) |
| Add a (predefined) ParametersSet object (via its owning pointer) to the current Conformation object. More... | |
| virtual core::Size | n_parameters_sets () const |
| Get the number of parameters sets defined for this Conformation. More... | |
| virtual void | clear_parameters_set_list () |
| Delete the list of ParametersSetOP objects. More... | |
| virtual ParametersSetOP | parameters_set (core::Size const index) |
| Access one of the ParametersSets objects linked to this Conformation. More... | |
| virtual 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... | |
| 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]> 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... | |
| 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 |
| void | insert_ideal_geometry_at_polymer_bond (Size seqpos) |
| void | insert_ideal_geometry_at_residue_connection (Size pos1, Size connid1) |
| void | update_actcoords () |
| void | update_actcoord (Size resid) |
| void | update_orbital_coords (Residue &rsd) const |
| void | update_orbital_coords (Size resid) |
| DOF_ID | dof_id_from_torsion_id (TorsionID const &id) const |
| id::AtomID | jump_atom_id (int 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... | |
| void | update_domain_map (DomainMap &domain_map) const |
| Generate a domain_map from the current dof/xyz moved data. More... | |
| bool | structure_moved () const |
| has the structure moved since the last call to reset_move_data or reset_structure_moved More... | |
| void | reset_structure_moved () const |
| reset the structure_moved_ bool More... | |
| void | reset_move_data () |
| forget all the structure modifications 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... | |
Private Member Functions | |
| core::Size | get_upstream_vrt (core::Size seqpos) const |
Private Attributes | |
| SymmetryInfoOP | symm_info_ |
| std::map< char, utility::vector1 < numeric::HomogeneousTransform < core::Real > > > | 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 core::conformation::symmetry::SymmetryInfo::clone(), symm_info_, and Tsymm_.
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virtual |
References core::conformation::Conformation::clear().
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virtual |
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().
| PointPosition core::conformation::symmetry::SymmetricConformation::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.
References recalculate_transforms(), symm_info_, and Tsymm_.
Referenced by append_residue_by_jump(), batch_set_xyz(), insert_conformation_by_jump(), replace_residue(), and set_xyz().
| PointPosition core::conformation::symmetry::SymmetricConformation::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)
References symm_info_, and Tsymm_.
Referenced by core::scoring::methods::RG_Energy_Fast::eval_atom_derivative().
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virtual |
Symmetric batch_set_xyz.
Reimplemented from core::conformation::Conformation.
References apply_transformation(), core::conformation::Conformation::batch_set_xyz(), core::sequence::end, symm_info_, core::conformation::symmetry::TR(), and Tsymm_.
|
virtual |
make a copy of this conformation( allocate actual memory for it )
Reimplemented from core::conformation::Conformation.
References symm_info_, and SymmetricConformation().
|
virtual |
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::conformation::Residue::atoms(), core::conformation::change_cys_state(), core::chemical::DISULFIDE, core::chemical::FA_STANDARD, core::conformation::find_neighbors(), core::chemical::ResidueType::has(), 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::conformation::Conformation::residue(), core::chemical::ResidueType::residue_connection_id_for_atom(), core::conformation::Conformation::residue_type(), core::conformation::Conformation::residues_, core::conformation::Conformation::size(), symm_info_, core::conformation::symmetry::TR(), core::conformation::Residue::type(), and core::conformation::Atom::xyz().
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virtual |
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().
|
inlinevirtual |
FoldTree access.
Reimplemented from core::conformation::Conformation.
References core::conformation::Conformation::fold_tree().
Referenced by append_residue_by_jump(), get_upstream_vrt(), insert_conformation_by_jump(), recalculate_transforms(), set_dof(), and set_jump().
|
virtual |
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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virtual |
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_.
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private |
|
virtual |
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().
| Conformation & core::conformation::symmetry::SymmetricConformation::operator= | ( | SymmetricConformation const & | src | ) |
copy constructor
operator=
operator
References core::conformation::Conformation::operator=(), symm_info_, and Tsymm_.
Referenced by operator=().
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equals operator. Must override this, since the operator= that takes a SymmetricConformation will not be used if both references are of type Conformation.
Reimplemented from core::conformation::Conformation.
References operator=(), and core::conformation::Conformation::operator=().
| void core::conformation::symmetry::SymmetricConformation::recalculate_transforms | ( | ) |
References core::conformation::Conformation::aa(), core::chemical::aa_vrt, core::conformation::Residue::atom(), core::conformation::ResidueFactory::create_residue(), core::kinematics::FoldTree::downstream_jump_residue(), fold_tree(), core::kinematics::FoldTree::num_jump(), core::conformation::Conformation::residue(), core::conformation::Conformation::size(), symm_info_, Tsymm_, core::kinematics::FoldTree::upstream_jump_residue(), protocols::comparative_modeling::features::X, core::conformation::Atom::xyz(), and core::chemical::element::Y.
Referenced by apply_transformation(), get_transformation(), 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 core::conformation::Conformation::aa(), core::chemical::aa_vrt, apply_transformation(), core::conformation::Residue::natoms(), core::conformation::Conformation::replace_residue(), core::conformation::Conformation::residue(), core::conformation::Residue::set_xyz(), symm_info_, core::conformation::symmetry::TR(), Tsymm_, and core::conformation::Residue::xyz().
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symmetry-safe replace residue
References core::conformation::Conformation::aa(), core::chemical::aa_vrt, apply_transformation(), core::conformation::Residue::natoms(), core::conformation::Conformation::replace_residue(), core::conformation::Conformation::residue(), core::conformation::Residue::set_xyz(), symm_info_, core::conformation::symmetry::TR(), Tsymm_, and core::conformation::Residue::xyz().
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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(), core::id::AtomID::rsd(), core::conformation::Conformation::set_bond_angle(), symm_info_, core::conformation::symmetry::TR(), and Tsymm_.
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BOND LENGTHS.
Reimplemented from core::conformation::Conformation.
References core::id::AtomID::atomno(), core::id::AtomID::rsd(), core::conformation::Conformation::set_bond_length(), symm_info_, core::conformation::symmetry::TR(), and Tsymm_.
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DOF.
Reimplemented from core::conformation::Conformation.
References 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_, core::conformation::symmetry::TR(), and Tsymm_.
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set a jump
JUMPS.
JUMPS
Reimplemented from core::conformation::Conformation.
References core::conformation::Conformation::jump_atom_id(), core::conformation::Conformation::set_jump(), symm_info_, core::conformation::symmetry::TR(), and Tsymm_.
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set a jump
Reimplemented from core::conformation::Conformation.
References fold_tree(), core::conformation::Conformation::jump_atom_id(), core::conformation::Conformation::set_jump(), symm_info_, core::conformation::symmetry::TR(), and Tsymm_.
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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 core::conformation::Conformation::set_torsion(), symm_info_, core::conformation::Conformation::torsion(), core::conformation::symmetry::TR(), and Tsymm_.
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TORSION ANGLES.
Reimplemented from core::conformation::Conformation.
References core::id::AtomID::atomno(), core::id::AtomID::rsd(), core::conformation::Conformation::set_torsion_angle(), symm_info_, core::conformation::symmetry::TR(), and Tsymm_.
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Symmetric set_xyz.
Reimplemented from core::conformation::Conformation.
References apply_transformation(), core::sequence::end, core::id::AtomID::rsd(), core::conformation::Conformation::set_xyz(), symm_info_, core::conformation::symmetry::TR(), and Tsymm_.
| SymmetryInfoCOP core::conformation::symmetry::SymmetricConformation::Symmetry_Info | ( | ) | const |
References symm_info_.
Referenced by protocols::hybridization::add_non_protein_cst(), protocols::simple_moves::AddConstraintsToCurrentConformationMover::apply(), protocols::electron_density::DensityMorphingMover::apply(), protocols::electron_density::ScaleMapIntensities::apply(), protocols::electron_density::ReportFSC::apply(), protocols::symmetric_docking::SymFoldandDockSlideTrialMover::apply(), protocols::simple_moves::symmetry::SymmetricRMSMover::apply(), protocols::protein_interface_design::movers::SaveAndRetrieveSidechains::apply(), protocols::matdes::SymDofMover::apply(), protocols::symmetric_docking::SymFoldandDockRbTrialMover::apply(), protocols::simple_moves::ReturnSidechainMover::apply(), protocols::hybridization::CartesianSampler::apply(), protocols::simple_moves::symmetry::SymDockingInitialPerturbation::apply(), protocols::hybridization::CartesianHybridize::apply(), protocols::toolbox::task_operations::SeqprofConsensusOperation::apply(), protocols::simple_moves::ReportEffectivePKA::apply(), protocols::relax::ClassicRelax::apply(), protocols::simple_moves::symmetry::SymDockingSlideIntoContact::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::idealize::IdealizeMover::apply(), protocols::hybridization::HybridizeProtocol::apply(), protocols::symmetric_docking::membrane::MPSymDockMover::apply(), protocols::simple_moves::symmetry::FaSymDockingSlideTogether::apply(), protocols::hybridization::CartesianSampler::apply_constraints(), protocols::hybridization::CartesianHybridize::apply_frame(), protocols::idealize::basic_idealize(), protocols::electron_density::BfactorMultifunc::BfactorMultifunc(), protocols::symmetric_docking::SymDockProtocol::calc_interaction_energy(), protocols::symmetric_docking::SymDockProtocol::calc_rms(), protocols::hybridization::HybridizeProtocol::check_and_create_fragments(), protocols::cryst::ReportGradientsMover::compute(), protocols::simple_filters::SymmetricMotifFilter::compute_d2(), core::pack::rotamer_set::symmetry::SymmetricRotamerSet_::compute_one_body_energies(), core::scoring::symmetry::SymmetricScoreFunction::correct_finalize_score(), core::pack::create_packer_graph(), core::scoring::electron_density::ElectronDensity::dCCdBs(), protocols::electron_density::BfactorMultifunc::dfunc(), protocols::rigid::MovePoseToMembraneCenterMover::estimate_membrane_center(), core::scoring::methods::ChainbreakEnergy::eval_atom_derivative(), core::scoring::methods::RG_Energy_Fast::eval_atom_derivative(), core::scoring::symmetry::SymmetricScoreFunction::eval_long_range_twobody_energies(), core::scoring::symmetry::SymmetricScoreFunction::eval_twobody_neighbor_energies(), core::pose::symmetry::extract_asymmetric_unit(), core::pose::symmetry::extract_asymmetric_unit_pdb_info(), core::scoring::symmetry::SymmetricEnergies::fill_point_graph(), core::pack::rotamer_set::symmetry::SymmetricRotamerSets::final_visit_to_edge(), core::scoring::methods::ChainbreakEnergy::finalize_total_energy(), core::scoring::methods::D2H_SA_Energy::finalize_total_energy(), core::scoring::methods::MembraneLipo::finalize_total_energy(), protocols::electron_density::find_best_anchor(), core::pose::symmetry::find_new_symmetric_jump_residues(), protocols::hybridization::generate_centroid_constraints(), core::conformation::symmetry::get_asymm_unit_fold_tree(), protocols::hybridization::get_num_residues_nonvirt(), protocols::hybridization::get_num_residues_prot(), core::util::getMLweight(), core::util::getMLweight_cart(), core::scoring::SecondaryStructurePotential::hspair(), protocols::hybridization::FragmentBiasAssigner::init(), protocols::floppy_tail::FloppyTailMover::init_on_new_input(), protocols::hybridization::HybridizeFoldtreeDynamic::initialize(), protocols::hybridization::HybridizeProtocol::initialize_and_sample_loops(), core::scoring::symmetry::SymmetricScoreFunction::intersubunit_hbond_energy(), core::optimization::symmetry::SymAtomTreeMinimizer::make_assymetric_movemap(), core::pack::make_new_symmetric_PackerTask_by_intersection(), core::pack::make_new_symmetric_PackerTask_by_union(), core::pose::symmetry::make_residue_mask_symmetric(), core::optimization::symmetry::SymAtomTreeMinimizer::make_semisymmetric_movemap(), core::pose::symmetry::make_symmetric_movemap(), core::pack::make_symmetric_PackerTask_by_truncation(), protocols::simple_moves::symmetry::SymPackRotamersMover::make_symmetric_task(), protocols::simple_moves::symmetry::SymRotamerTrialsMover::make_symmetric_task(), protocols::simple_moves::symmetry::SymEnergyCutRotamerTrialsMover::make_symmetric_task(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD_Moves::model_loop(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD::model_loop(), core::scoring::MembranePotential::non_helix_in_membrane_penalty(), protocols::cryst::ReportGradientsMover::normalization(), protocols::electron_density::BfactorMultifunc::operator()(), protocols::comparative_modeling::pick_loops_chainbreak(), core::pack::rotamer_set::symmetry::SymmetricRotamerSets::precompute_two_body_energies(), core::pack::rotamer_set::symmetry::SymmetricRotamerSets::prepare_symm_otf_interaction_graph(), protocols::simple_filters::AlaScan::report_symmetry(), core::scoring::symmetry::SymmetricEnergies::require_context_graph_(), core::scoring::electron_density::ElectronDensity::rescale_fastscoring_temp_bins(), core::scoring::methods::MembraneCenPairEnergy::residue_pair_energy(), core::scoring::membrane::MPPairEnergy::residue_pair_energy(), core::optimization::symmetry::SymAtomTreeMinimizer::run(), core::scoring::MembranePotential::score_normal_center(), core::pose::symmetry::sealed_symmetric_fold_tree(), protocols::symmetric_docking::SymDockingLowRes::set_default_protocol(), protocols::symmetric_docking::SymDockingHiRes::set_dock_mcm_protocol(), protocols::symmetric_docking::SymDockingHiRes::set_dock_ppk_protocol(), core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::set_pose(), core::scoring::symmetry::SymmetricScoreFunction::set_symmetric_cenlist(), core::scoring::symmetry::SymmetricScoreFunction::set_symmetric_residue_neighbors_hbonds(), protocols::simple_moves::symmetry::SymmetrySlider::setup(), protocols::hybridization::FoldTreeHybridize::setup_foldtree(), core::scoring::methods::EnvSmoothEnergy::setup_for_derivatives(), core::scoring::symmetry::SymmetricScoreFunction::setup_for_derivatives(), core::scoring::symmetry::SymmetricScoreFunction::setup_for_minimizing(), protocols::idealize::IdealizeMover::setup_idealize_constraints(), protocols::membrane::symmetry::SymmetricAddMembraneMover::setup_membrane_virtual(), core::scoring::SecondaryStructurePotential::sheets_from_dimers(), core::conformation::symmetry::shift_jump_numbers_in_dofs(), core::conformation::symmetry::show_foldtree(), protocols::simple_moves::symmetry::SymmetrySlider::slide(), protocols::simple_moves::symmetry::SymmetrySlider::slide_away(), core::scoring::SecondaryStructurePotential::sspair(), core::util::switch_to_residue_type_set(), core::scoring::sym_rmsd_with_super_subset(), core::pack::symmetric_pack_rotamers_run(), core::pack::symmetric_repackable_residues(), core::pack::symmetric_rotamer_trials(), core::scoring::symmetry::SymmetricScoreFunction::symmetrical_allow_hbonds(), core::conformation::symmetry::symmetrize_fold_tree(), protocols::membrane::symmetry::symmetrize_spans(), protocols::electron_density::symmetrizeBfactors(), core::pose::symmetry::symmetry_info(), core::scoring::MembranePotential::termini_penalty(), protocols::simple_moves::ddG::unbind(), core::scoring::symmetry::SymmetricEnergies::update_neighbor_links(), and protocols::simple_moves::symmetry::SymmetrySlider::very_far_away().
| SymmetryInfoOP core::conformation::symmetry::SymmetricConformation::Symmetry_Info | ( | ) |
References symm_info_.
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Referenced by append_residue_by_jump(), apply_transformation(), apply_transformation_norecompute(), batch_set_xyz(), clone(), detect_disulfides(), fold_tree(), get_residue_mask(), get_residue_weight(), get_transformation(), insert_conformation_by_jump(), operator=(), recalculate_transforms(), replace_residue(), set_bond_angle(), set_bond_length(), set_dof(), set_jump(), set_secstruct(), set_torsion(), set_torsion_angle(), set_xyz(), SymmetricConformation(), and Symmetry_Info().
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Referenced by apply_transformation(), apply_transformation_norecompute(), batch_set_xyz(), get_transformation(), operator=(), recalculate_transforms(), replace_residue(), set_bond_angle(), set_bond_length(), set_dof(), set_jump(), set_torsion(), set_torsion_angle(), set_xyz(), and SymmetricConformation().
1.8.7