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core::conformation::symmetry::SymmetricConformation Class Reference

A symmetric conformation: has an additional data member "SymmetryInfo" class. More...

#include <SymmetricConformation.hh>

Inheritance diagram for core::conformation::symmetry::SymmetricConformation:
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Collaboration diagram for core::conformation::symmetry::SymmetricConformation:
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Public Member Functions

 SymmetricConformation ()
 Default CTOR. More...
 
 SymmetricConformation (Conformation const &conf, SymmetryInfo const &symm_info)
 Default CTOR. More...
 
 SymmetricConformation (SymmetricConformation const &src)
 copy constructor More...
 
Conformationoperator= (SymmetricConformation const &src)
 operator More...
 
ConformationOP clone () const
 
virtual bool same_type_as_me (Conformation const &other, bool recurse) const
 
SymmetryInfoCOP Symmetry_Info () const
 
SymmetryInfoOP Symmetry_Info ()
 
virtual void set_dof (DOF_ID const &id, Real const setting)
 DOF. More...
 
void set_secstruct (Size const seqpos, char const setting)
 set the secondary structure of a sequence position More...
 
virtual void set_torsion (TorsionID const &id, Real const setting)
 BONDS/TORSIONS. More...
 
virtual void set_jump (int const jump_number, Jump const &new_jump)
 set a jump More...
 
virtual void set_jump_now (int const jump_number, Jump const &new_jump)
 set a jump and force immediate calculation of affected XYZ coords 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 const setting)
 BOND ANGLES. More...
 
virtual void set_bond_length (AtomID const &atom1, AtomID const &atom2, Real const setting)
 BOND LENGTHS. More...
 
virtual void set_torsion_angle (AtomID const &atom1, AtomID const &atom2, AtomID const &atom3, AtomID const &atom4, Real const setting)
 TORSION ANGLES. More...
 
virtual utility::vector1< boolget_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 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)
 
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)
 Remap coordinate X from resid i's frame to resid j's frame. More...
 
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 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; clones this append to all copies. 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="")
 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 ()
 HIGHLY HIGHLY ILLEGAL ACCESS GRANTED TO CONFORMATION DATA. This function will be removed very very shortly. More...
 
virtual ~Conformation ()
 default destructor More...
 
 Conformation (Conformation const &src)
 copy constructor More...
 
virtual Conformationoperator= (Conformation const &src)
 operator 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...
 
Size chain_end (Size const chain) const
 Returns the position number of the last residue in <chain> More...
 
Size chain_begin (Size const chain) const
 Returns the position number of the first residue in <chain> More...
 
Size num_chains () const
 Returns the number of chains. More...
 
char secstruct (Size const seqpos) const
 Returns the secondary structure the position <seqpos> More...
 
AtomTree const & atom_tree () const
 Returns the conformation's AtomTree. 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 const seqpos)
 Marks <seqpos> as the end of a new chain. More...
 
void delete_chain_ending (Size const 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...
 
chemical::AA const & aa (Size const seqpos) const
 Returns the AA enum for position <seqpos> More...
 
Residue const & residue (Size const seqpos) const
 access one of the residues; this access is inlined, since otherwise it shows up in the profiler. This will call non-inlined refold methods if necessary. More...
 
chemical::ResidueType const & residue_type (Size const seqpos) const
 access one of the residue's types – avoids coord/torsion update More...
 
void insert_residue_by_jump (Residue const &new_rsd_in, Size const 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 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...
 
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...
 
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...
 
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...
 
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, utility::vector1< std::pair< std::string, std::string > > const &atom_pairs)
 funtion to replace a residue based on superposition on More...
 
void delete_polymer_residue (Size const seqpos)
 Delete polymer residue at the given sequence position. More...
 
void delete_residue_slow (Size const seqpos)
 Slow method that relies on FoldTree::delete_seqpos, rebuilds atomtree, can handle jumps/root residue. More...
 
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 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 copy_segment (Size const size, Conformation const &src, Size const begin, Size const src_begin)
 copy a stretch of coordinates/torsions from another Conformation More...
 
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 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
 
void rebuild_residue_connection_dependent_atoms (Size const seqpos, Size const connid)
 
ResidueCAPs const_residues () const
 Inefficient – constructs copy of residues_. More...
 
Real dof (DOF_ID const &id) const
 Returns the AtomTree degree of freedom (DOF) <id> More...
 
Real torsion (TorsionID const &id) const
 Returns the torsion angle <id> More...
 
void insert_ideal_geometry_at_polymer_bond (Size const seqpos)
 
void insert_ideal_geometry_at_residue_connection (Size const pos1, Size const connid1)
 
void insert_fragment (id::StubID const &instub_id, FragRT const &outstub_transforms, FragXYZ const &frag_xyz)
 
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]> More...
 
Real bond_length (AtomID const &atom1, AtomID const &atom2) const
 Returns the bond length between <atom1> and <atom2> More...
 
const Jumpjump (int const jump_number) const
 Returns the Jump with jump number <jump_number> More...
 
const Jumpjump (AtomID const &id) const
 access a jump More...
 
void set_polymeric_connection (Size res_id_lower, Size res_id_upper)
 identify polymeric connections More...
 
void update_polymeric_connection (Size const lower_seqpos)
 Update the polymer connection status between lower_seqpos and lower_seqpos+1 based on chainID's and termini. More...
 
void detect_bonds ()
 
void detect_pseudobonds ()
 
void fix_disulfides (utility::vector1< std::pair< Size, Size > > disulf_bonds)
 Assigns disulfide bonds based on a pre-determined list. More...
 
kinematics::Stub upstream_jump_stub (int const 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 const jump_number) const
 The upstream and downstream Stubs are the coordinate frames between which this jump is transforming. 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 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 const 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...
 
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...
 
void clear ()
 clear data More...
 
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...
 
AtomID inter_residue_connection_partner (Size const seqpos, int const connection_index) const
 This returns the AtomID of the atom in the other residue to which the "connection_index"-th. 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 const pos, Size const atomno) 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 const flag) const
 wait for stdin after sending a GeneralEvent signal More...
 
bool debug_pause () const
 waiting for stdin after sending a GeneralEvent signal? 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...
 
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
 
void recalculate_transforms ()
 

Private Attributes

SymmetryInfoOP symm_info_
 
utility::vector1
< numeric::HomogeneousTransform
< core::Real > > 
Tsymm_
 

Additional Inherited Members

- Public Types inherited from core::conformation::Conformation
typedef kinematics::Jump Jump
 
typedef kinematics::FoldTree FoldTree
 
typedef kinematics::FoldTreeOP FoldTreeOP
 
typedef kinematics::AtomTree AtomTree
 
typedef kinematics::AtomTreeOP AtomTreeOP
 
typedef id::AtomID AtomID
 
typedef id::AtomID_Mask AtomID_Mask
 
typedef id::DOF_ID DOF_ID
 
typedef id::TorsionID TorsionID
 
typedef kinematics::DomainMap DomainMap
 
typedef
core::conformation::signals::ConnectionEvent 
ConnectionEvent
 
typedef
core::conformation::signals::GeneralEvent 
GeneralEvent
 
typedef
core::conformation::signals::IdentityEvent 
IdentityEvent
 
typedef
core::conformation::signals::LengthEvent 
LengthEvent
 
typedef
core::conformation::signals::XYZEvent 
XYZEvent
 
typedef std::map< id::AtomID,
Vector
FragXYZ
 
typedef std::map< id::StubID,
kinematics::RT
FragRT
 
- Protected Attributes inherited from core::conformation::Conformation
ResidueOPs residues_
 container of Residues More...
 

Detailed Description

A symmetric conformation: has an additional data member "SymmetryInfo" class.

Handles symmetrizing of some of the conformation-changing methods of Conformation

Constructor & Destructor Documentation

core::conformation::symmetry::SymmetricConformation::SymmetricConformation ( )

Default CTOR.

References Tsymm_.

Referenced by clone().

core::conformation::symmetry::SymmetricConformation::SymmetricConformation ( Conformation const &  conf,
SymmetryInfo const &  symm_info 
)

Default CTOR.

References Tsymm_.

core::conformation::symmetry::SymmetricConformation::SymmetricConformation ( SymmetricConformation const &  src)

copy constructor

core::conformation::symmetry::SymmetricConformation::~SymmetricConformation ( )
virtual

Member Function Documentation

void core::conformation::symmetry::SymmetricConformation::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 
)
virtual
PointPosition core::conformation::symmetry::SymmetricConformation::apply_transformation ( PointPosition  Xin,
core::Size  residfrom,
core::Size  residto 
)

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().

void core::conformation::symmetry::SymmetricConformation::batch_set_xyz ( utility::vector1< AtomID > const &  ids,
utility::vector1< PointPosition > const &  positions 
)
virtual
ConformationOP core::conformation::symmetry::SymmetricConformation::clone ( ) const
virtual

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

Reimplemented from core::conformation::Conformation.

References SymmetricConformation().

void core::conformation::symmetry::SymmetricConformation::detect_disulfides ( )
virtual
void core::conformation::symmetry::SymmetricConformation::fold_tree ( FoldTree const &  fold_tree_in)
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().

virtual FoldTree const& core::conformation::symmetry::SymmetricConformation::fold_tree ( ) const
inlinevirtual
utility::vector1< bool > core::conformation::symmetry::SymmetricConformation::get_residue_mask ( ) const
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_.

core::Real core::conformation::symmetry::SymmetricConformation::get_residue_weight ( core::Size  ,
core::Size   
) const
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_.

core::Size core::conformation::symmetry::SymmetricConformation::get_upstream_vrt ( core::Size  seqpos) const
private
void core::conformation::symmetry::SymmetricConformation::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 = "" 
)
virtual
Conformation & core::conformation::symmetry::SymmetricConformation::operator= ( SymmetricConformation const &  src)

operator

operator=

References core::conformation::Conformation::operator=(), symm_info_, and Tsymm_.

void core::conformation::symmetry::SymmetricConformation::recalculate_transforms ( )
private
void core::conformation::symmetry::SymmetricConformation::replace_residue ( Size const  seqpos,
Residue const &  new_rsd_in,
bool const  orient_backbone 
)
virtual
void core::conformation::symmetry::SymmetricConformation::replace_residue ( Size const  seqpos,
Residue const &  new_rsd,
utility::vector1< std::pair< std::string, std::string > > const &  atom_pairs 
)
virtual
bool core::conformation::symmetry::SymmetricConformation::same_type_as_me ( Conformation const &  other,
bool  recurse 
) const
virtual

determine the type of the ConformationOP

Reimplemented from core::conformation::Conformation.

References core::conformation::Conformation::same_type_as_me().

void core::conformation::symmetry::SymmetricConformation::set_bond_angle ( AtomID const &  atom1,
AtomID const &  atom2,
AtomID const &  atom3,
Real const  setting 
)
virtual
void core::conformation::symmetry::SymmetricConformation::set_bond_length ( AtomID const &  atom1,
AtomID const &  atom2,
Real const  setting 
)
virtual
void core::conformation::symmetry::SymmetricConformation::set_dof ( DOF_ID const &  id,
Real const  setting 
)
virtual
void core::conformation::symmetry::SymmetricConformation::set_jump ( int const  jump_number,
kinematics::Jump const &  new_jump 
)
virtual
void core::conformation::symmetry::SymmetricConformation::set_jump ( id::AtomID const &  id,
kinematics::Jump const &  new_jump 
)
virtual
void core::conformation::symmetry::SymmetricConformation::set_jump_now ( int const  jump_number,
kinematics::Jump const &  new_jump 
)
virtual
void core::conformation::symmetry::SymmetricConformation::set_secstruct ( Size const  seqpos,
char const  setting 
)
virtual

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().

void core::conformation::symmetry::SymmetricConformation::set_torsion ( id::TorsionID const &  id,
Real const  setting 
)
virtual
void core::conformation::symmetry::SymmetricConformation::set_torsion_angle ( AtomID const &  atom1,
AtomID const &  atom2,
AtomID const &  atom3,
AtomID const &  atom4,
Real const  setting 
)
virtual
void core::conformation::symmetry::SymmetricConformation::set_xyz ( AtomID const &  id,
PointPosition const &  position 
)
virtual
SymmetryInfoCOP core::conformation::symmetry::SymmetricConformation::Symmetry_Info ( ) const

References symm_info_.

Referenced by protocols::simple_moves::symmetry::SymmetricRMSMover::apply(), protocols::symmetric_docking::SymFoldandDockSlideTrialMover::apply(), protocols::protein_interface_design::movers::SaveAndRetrieveSidechains::apply(), protocols::simple_moves::ReturnSidechainMover::apply(), protocols::symmetric_docking::SymFoldandDockRbTrialMover::apply(), protocols::simple_moves::symmetry::SymDockingInitialPerturbation::apply(), protocols::toolbox::task_operations::SeqprofConsensusOperation::apply(), protocols::hybridization::HybridizeProtocol::apply(), protocols::relax::ClassicRelax::apply(), protocols::simple_moves::symmetry::SymDockingSlideIntoContact::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::idealize::IdealizeMover::apply(), protocols::simple_moves::symmetry::FaSymDockingSlideTogether::apply(), protocols::hybridization::CartesianSampler::apply_frame(), protocols::hybridization::CartesianHybridize::apply_frame(), protocols::idealize::basic_idealize(), protocols::symmetric_docking::SymDockProtocol::calc_interaction_energy(), protocols::symmetric_docking::SymDockProtocol::calc_rms(), protocols::hybridization::HybridizeProtocol::check_and_create_fragments(), protocols::simple_filters::SymmetricMotifFilter::compute_d2(), protocols::hybridization::CartesianSampler::compute_fragment_bias(), core::pack::rotamer_set::symmetry::SymmetricRotamerSet_::compute_one_body_energies(), core::scoring::symmetry::SymmetricScoreFunction::correct_finalize_score(), core::pack::create_packer_graph(), protocols::rigid::MovePoseToMembraneCenterMover::estimate_membrane_center(), core::scoring::methods::ChainbreakEnergy::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::MetalloPlacementEnergy::finalize_total_energy(), core::scoring::methods::MembraneLipo::finalize_total_energy(), core::scoring::methods::ChainbreakEnergy::finalize_total_energy(), core::pose::symmetry::find_new_symmetric_jump_residues(), core::conformation::symmetry::get_asymm_unit_fold_tree(), protocols::hybridization::get_num_residues_nonvirt(), core::scoring::SecondaryStructurePotential::hspair(), 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::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::methods::MembraneCenPairEnergy::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::symmetry::SymmetricScoreFunction::setup_for_derivatives(), core::scoring::symmetry::SymmetricScoreFunction::setup_for_minimizing(), protocols::idealize::IdealizeMover::setup_idealize_constraints(), 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::scoring::sym_rmsd_with_super_subset(), protocols::simple_moves::ddG::symm_ddG(), core::pack::symmetric_pack_rotamers_run(), core::pack::symmetric_repackable_residues(), core::pack::symmetric_rotamer_trials(), core::pack::task::operation::RestrictToInterface::symmetric_task(), core::scoring::symmetry::SymmetricScoreFunction::symmetrical_allow_hbonds(), core::conformation::symmetry::symmetrize_fold_tree(), core::pose::symmetry::symmetry_info(), core::scoring::MembranePotential::termini_penalty(), 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_.

Member Data Documentation

SymmetryInfoOP core::conformation::symmetry::SymmetricConformation::symm_info_
private
utility::vector1< numeric::HomogeneousTransform< core::Real > > core::conformation::symmetry::SymmetricConformation::Tsymm_
private

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