Rosetta Core  2014.35
Public Member Functions | Private Member Functions | Private Attributes | List of all members
core::conformation::symmetry::SymmetricConformation Class Reference

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...
 
 SymmetricConformation (SymmetricConformation const &src)
 copy constructor More...
 
Conformationoperator= (SymmetricConformation const &src)
 operator More...
 
virtual Conformationoperator= (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 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 (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, bool const quiet=false)
 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, 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 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 ()
 constructor More...
 
virtual ~Conformation ()
 default destructor More...
 
 Conformation (Conformation const &src)
 copy constructor 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...
 
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 const setting)
 Set whether this conformation contains any carbohydrate 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...
 
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...
 
char secstruct (Size const 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 const seqpos) const
 Returns the AA enum for position <seqpos> More...
 
Residue const & residue (Size const seqpos) const
 access one of the residues More...
 
chemical::ResidueType const & residue_type (Size const seqpos) const
 access one of the residue's types – avoids coord/torsion update More...
 
ResidueCAPs const_residues () const
 Inefficient – constructs copy of residues_. 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 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. 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)
 function to replace a residue based on superposition on the specified input atom pairs 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 detect_bonds ()
 
void detect_pseudobonds ()
 
void declare_chemical_bond (Size const seqpos1, std::string const &atom_name1, Size const seqpos2, std::string const &atom_name2)
 Declare that a chemical bond exists between two residues. More...
 
void rebuild_polymer_bond_dependent_atoms_this_residue_only (Size const seqpos)
 Rebuilds the atoms that are depenent on polymer bonds for the specified residue only. 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 rebuild_residue_connection_dependent_atoms (Size const seqpos, Size const connid)
 
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 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 const pos, Size const 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 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...
 
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 const lower_seqpos, bool const 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 const lower_seqpos, Size const lr_conn_id, Size const upper_seqpos, Size const 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...
 
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 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
 Returns the torsion angle <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 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...
 
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 const seqpos)
 
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)
 
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...
 
bool get_jump_atom_ids (core::Size const 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 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...
 
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_
 

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

References Tsymm_.

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,
bool  rotationonly = false 
)
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 numeric::HomogeneousTransform< T >::inverse(), runtime_assert, numeric::HomogeneousTransform< T >::set_identity_transform(), symm_info_, and Tsymm_.

Referenced by core::scoring::methods::RG_Energy_Fast::eval_atom_derivative().

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_.

Referenced by operator=().

Conformation & core::conformation::symmetry::SymmetricConformation::operator= ( Conformation const &  src)
virtual

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 ( )
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_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,
bool const  quiet = false 
)
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 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(), 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::MetalloPlacementEnergy::finalize_total_energy(), core::scoring::methods::MembraneLipo::finalize_total_energy(), core::pose::symmetry::find_new_symmetric_jump_residues(), core::conformation::symmetry::get_asymm_unit_fold_tree(), core::util::getMLweight(), core::util::getMLweight_cart(), core::scoring::SecondaryStructurePotential::hspair(), 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(), core::scoring::MembranePotential::non_helix_in_membrane_penalty(), core::pack::rotamer_set::symmetry::SymmetricRotamerSets::precompute_two_body_energies(), core::pack::rotamer_set::symmetry::SymmetricRotamerSets::prepare_symm_otf_interaction_graph(), 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(), core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::set_pose(), core::scoring::symmetry::SymmetricScoreFunction::set_symmetric_cenlist(), core::scoring::symmetry::SymmetricScoreFunction::set_symmetric_residue_neighbors_hbonds(), core::scoring::methods::EnvSmoothEnergy::setup_for_derivatives(), core::scoring::symmetry::SymmetricScoreFunction::setup_for_derivatives(), core::scoring::symmetry::SymmetricScoreFunction::setup_for_minimizing(), core::scoring::SecondaryStructurePotential::sheets_from_dimers(), core::conformation::symmetry::shift_jump_numbers_in_dofs(), core::conformation::symmetry::show_foldtree(), 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::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(), and core::scoring::symmetry::SymmetricEnergies::update_neighbor_links().

SymmetryInfoOP core::conformation::symmetry::SymmetricConformation::Symmetry_Info ( )

References symm_info_.

Member Data Documentation

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

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