Rosetta 3.4
Public Member Functions
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:
Inheritance graph
[legend]
Collaboration diagram for core::conformation::symmetry::SymmetricConformation:
Collaboration graph
[legend]

List of all members.

Public Member Functions

 SymmetricConformation ()
 Default CTOR.
 SymmetricConformation (Conformation const &conf, SymmetryInfo const &symm_info)
 Default CTOR.
 SymmetricConformation (SymmetricConformation const &src)
 copy constructor
Conformationoperator= (SymmetricConformation const &src)
 operator
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.
void set_secstruct (Size const seqpos, char const setting)
 set the secondary structure of a sequence position
virtual void set_torsion (TorsionID const &id, Real const setting)
 BONDS/TORSIONS.
virtual void set_jump (int const jump_number, Jump const &new_jump)
 set a jump
virtual void set_jump_now (int const jump_number, Jump const &new_jump)
 set a jump and force immediate calculation of affected XYZ coords
virtual void set_jump (AtomID const &id, Jump const &new_jump)
 set a jump
virtual void set_bond_angle (AtomID const &atom1, AtomID const &atom2, AtomID const &atom3, Real const setting)
 BOND ANGLES.
virtual void set_bond_length (AtomID const &atom1, AtomID const &atom2, Real const setting)
 BOND LENGTHS.
virtual void set_torsion_angle (AtomID const &atom1, AtomID const &atom2, AtomID const &atom3, AtomID const &atom4, Real const setting)
 TORSION ANGLES.
virtual utility::vector1< boolget_residue_mask () const
virtual Real get_residue_weight (core::Size resid1, core::Size resid2) const
 returns a residue-pair weight
virtual void replace_residue (Size const seqpos, Residue const &new_rsd, bool const orient_backbone)
 replace residue
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
virtual FoldTree const & fold_tree () const
 FoldTree access.
numeric::HomogeneousTransform
< core::Real
get_transformation (core::Size resid)
 Get the transformation controlling resid i.
PointPosition apply_transformation (PointPosition Xin, core::Size residfrom, core::Size residto)
 Remap coordinate X from resid i's frame to resid j's frame.
virtual void set_xyz (AtomID const &id, PointPosition const &position)
 Symmetric set_xyz.
virtual void batch_set_xyz (utility::vector1< AtomID > const &ids, utility::vector1< PointPosition > const &positions)
 Symmetric batch_set_xyz.
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.
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.

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.

Referenced by clone().

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

Default CTOR.

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.

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::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 fold_tree(), core::conformation::symmetry::get_asymm_unit_fold_tree(), and core::kinematics::FoldTree::num_jump().

virtual FoldTree const& core::conformation::symmetry::SymmetricConformation::fold_tree ( ) const [inline, virtual]
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.

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.

numeric::HomogeneousTransform< core::Real > core::conformation::symmetry::SymmetricConformation::get_transformation ( core::Size  resid)

Get the transformation controlling resid i.

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=

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]

set a jump and force immediate calculation of affected XYZ coords

Reimplemented from core::conformation::Conformation.

References core::conformation::Conformation::jump_atom_id(), set_jump(), and core::conformation::symmetry::TR().

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::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

Referenced by protocols::symmetric_docking::SymFoldandDockSlideTrialMover::apply(), protocols::symmetric_docking::SymFoldandDockRbTrialMover::apply(), protocols::simple_moves::symmetry::SymmetricRMSMover::apply(), protocols::simple_moves::symmetry::FaSymDockingSlideTogether::apply(), protocols::simple_moves::symmetry::SymDockingSlideIntoContact::apply(), protocols::simple_moves::symmetry::SymDockingInitialPerturbation::apply(), protocols::relax::ClassicRelax::apply(), protocols::idealize::IdealizeMover::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::comparative_modeling::hybridize::CartesianHybridize::apply_frame(), protocols::idealize::basic_idealize(), protocols::symmetric_docking::SymDockProtocol::calc_interaction_energy(), protocols::symmetric_docking::SymDockProtocol::calc_rms(), core::pack::rotamer_set::symmetry::SymmetricRotamerSet_::compute_one_body_energies(), core::scoring::symmetry::SymmetricScoreFunction::correct_finalize_score(), protocols::rigid::MovePoseToMembraneCenterMover::estimate_membrane_center(), 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::pack::rotamer_set::symmetry::SymmetricRotamerSets::final_visit_to_edge(), 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(), protocols::comparative_modeling::hybridize::HybridizeFoldtreeDynamic::initialize(), protocols::comparative_modeling::hybridize::HybridizeProtocol::initialize_and_sample_loops(), core::scoring::symmetry::SymmetricScoreFunction::intersubunit_hbond_energy(), core::optimization::symmetry::SymAtomTreeMinimizer::make_assymetric_movemap(), 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(), 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(), protocols::simple_filters::AlaScan::report_symmetry(), protocols::protein_interface_design::AlaScan::report_symmetry(), core::scoring::methods::MembraneCenPairEnergy::residue_pair_energy(), core::optimization::symmetry::SymAtomTreeMinimizer::run(), 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::scoring::symmetry::SymmetricScoreFunction::set_symmetric_cenlist(), protocols::scoring::Interface::set_symmetric_pack(), core::scoring::symmetry::SymmetricScoreFunction::set_symmetric_residue_neighbors_hbonds(), protocols::simple_moves::symmetry::SymmetrySlider::setup(), protocols::comparative_modeling::hybridize::FoldTreeHybridize::setup_foldtree(), core::scoring::symmetry::SymmetricScoreFunction::setup_for_derivatives(), core::scoring::symmetry::SymmetricScoreFunction::setup_for_minimizing(), core::conformation::symmetry::shift_jump_numbers_in_dofs(), protocols::simple_moves::symmetry::SymmetrySlider::slide(), protocols::simple_moves::symmetry::SymmetrySlider::slide_away(), 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(), and protocols::simple_moves::symmetry::SymmetrySlider::very_far_away().

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

The documentation for this class was generated from the following files:
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Defines