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core::conformation::symmetry Namespace Reference

Classes

class  SymDof
 
class  SymmData
 
class  SymmDataFactory
 
class  SymmDataLoader
 
class  SymmDataLoaderCreator
 
class  SymmDataOptions
 
class  SymmDataOptionsCreator
 
class  SymmetricConformation
 A symmetric conformation: has an additional data member "SymmetryInfo" class. More...
 
class  SymmetryInfo
 
class  SymSlideInfo
 
class  VirtualCoordinate
 
class  VirtualCoordinates
 

Typedefs

typedef
utility::pointer::owning_ptr
< SymDof > 		SymDofOP
 
typedef
utility::pointer::owning_ptr
< SymDof const > 		SymDofCOP
 
typedef numeric::xyzTransform
< Real > 		Xform
 
typedef numeric::xyzVector< Real > Vec
 
typedef numeric::xyzMatrix< Real > Mat
 
typedef vector1< pair< Size,
Real > > 		WtedClones
 
typedef
utility::pointer::owning_ptr
< SymmData > 		SymmDataOP
 
typedef
utility::pointer::owning_ptr
< SymmData const > 		SymmDataCOP
 
typedef
utility::pointer::owning_ptr
< SymmDataLoader > 		SymmDataLoaderOP
 
typedef
utility::pointer::owning_ptr
< SymmDataLoader const > 		SymmDataLoaderCOP
 
typedef
utility::pointer::owning_ptr
< SymmDataOptions > 		SymmDataOptionsOP
 
typedef
utility::pointer::owning_ptr
< SymmDataOptions const > 		SymmDataOptionsCOP
 
typedef
utility::pointer::owning_ptr
< SymmetricConformation > 		SymmetricConformationOP
 
typedef
utility::pointer::owning_ptr
< SymmetricConformation const > 		SymmetricConformationCOP
 
typedef
utility::pointer::owning_ptr
< SymmetryInfo > 		SymmetryInfoOP
 
typedef
utility::pointer::owning_ptr
< SymmetryInfo const > 		SymmetryInfoCOP
 
typedef
utility::pointer::owning_ptr
< SymSlideInfo > 		SymSlideInfoOP
 
typedef
utility::pointer::owning_ptr
< SymSlideInfo const > 		SymSlideInfoCOP
 
typedef
utility::pointer::owning_ptr
< VirtualCoordinate > 		VirtualCoordinateOP
 
typedef
utility::pointer::owning_ptr
< VirtualCoordinate const > 		VirtualCoordinateCOP
 

Enumerations

enum  dof_type {
  X_DOF = 1, Y_DOF, Z_DOF, X_ANGLE_DOF,
  Y_ANGLE_DOF, Z_ANGLE_DOF
}
 
enum  SlideType { SEQUENTIAL = 1, ORDERED_SEQUENTIAL, RANDOM }
 
enum  SlideCriteriaType { CEN_DOCK_SCORE = 1, FA_REP_SCORE, CONTACTS, TOTAL_NUM_CRITERIA }
 

Functions

std::ostream & operator<< (std::ostream &s, const SymDof &dof)
 
bool operator== (SymDof const &a, SymDof const &b)
 
bool operator!= (SymDof const &a, SymDof const &b)
 
static basic::Tracer TR ("core.conformation.symmetry.SymmData")
 
bool operator== (SymmData const &a, SymmData const &b)
 
static basic::Tracer TR ("core.conformation.symmetry.symmdatafactory")
 
static basic::Tracer TR ("core.conformation.symmetry.Conformation")
 
id::TorsionType guess_torsion_type_of_dof_id (id::DOF_ID const &id, Conformation const &conf)
 
template<class T >
void comma_strings_to_vector_map (std::istream &is, Size const nbase, std::map< Size, utility::vector1< T > > &clones, std::string tag="")
 
template<class T >
void comma_strings_to_map (std::istream &is, Size const nbase, std::map< Size, T > &clones, std::string tag="")
 
void comma_strings_to_map (std::istream &is, Size const nbase, std::map< Size, SymDof > &clones, std::string tag="")
 
void comma_strings_to_vector (std::istream &is, Size const nbase, utility::vector1< Size > &clones, std::string tag="")
 
template<class CloneType >
void vector_map_to_comma_strings (std::ostream &out, std::map< Size, utility::vector1< CloneType > > clones, std::string tag="")
 
template<class CloneType >
void map_to_comma_strings (std::ostream &out, std::map< Size, CloneType > clones, std::string tag="")
 
void map_to_comma_strings (std::ostream &out, std::map< Size, SymDof > clones, std::string tag="")
 
void vector_to_comma_strings (std::ostream &out, utility::vector1< Size > clones, std::string tag="")
 
std::istream & operator>> (std::istream &s, SymmetryInfo &symminfo)
 
std::ostream & operator<< (std::ostream &s, const SymmetryInfo &symminfo)
 
bool operator== (SymSlideInfo const &a, SymSlideInfo const &b)
 
bool operator!= (SymSlideInfo const &a, SymSlideInfo const &b)
 
static basic::Tracer TR ("core.conformation.symmetry.util")
 
static
numeric::random::RandomGenerator 		RG (408529)
 
Size fold_tree_entry_point (core::kinematics::FoldTree const &ft, Size lb_resi=0, Size ub_resi=0)
 
Size process_residue_request (conformation::Conformation const &src_conf, std::string input, Size lb_resi=0, Size ub_resi=0)
 
bool is_jump_intracomponent (std::map< char, std::pair< Size, Size > > chain2range, Size up, Size dn)
 
char which_component (std::map< char, std::pair< Size, Size > > chain2range, Size resi)
 
core::kinematics::FoldTree get_component_contiguous_foldtree (core::kinematics::FoldTree const &f_orig, std::map< char, std::pair< Size, Size > > const &)
 
std::map< char, std::pair
< Size, Size > > 		get_chain2range (Conformation const &src_conf, std::map< int, char > src_conf2pdb_chain)
 
bool is_symmetric (conformation::Conformation const &conf)
 
bool is_symmetric (conformation::symmetry::SymmetryInfo const &symminfo)
 
conformation::symmetry::SymmetricConformationOP setup_symmetric_conformation (conformation::Conformation &src_conformation, conformation::symmetry::SymmData &symmdata, std::map< int, char > src_conf2pdb_chain)
 
kinematics::FoldTree set_fold_tree_from_symm_data (conformation::Conformation &src_conformation, conformation::symmetry::SymmData &symmdata, std::map< int, char > src_conf2pdb_chain)
 
kinematics::FoldTree replaced_symmetric_foldtree_with_new_monomer (kinematics::FoldTree symm_f, conformation::symmetry::SymmetryInfo symmetry_info, kinematics::FoldTree monomer_f)
 
void recenter (conformation::Conformation &src_conformation, conformation::symmetry::SymmData &symmdata)
 
void shift_jump_numbers_in_dofs (conformation::Conformation &conformation, Size shift)
 
kinematics::FoldTree get_asymm_unit_fold_tree (core::conformation::Conformation const &conf)
 
void symmetrize_fold_tree (core::conformation::Conformation const &conf, kinematics::FoldTree &f)
 
void set_asymm_unit_fold_tree (core::conformation::Conformation &conf, kinematics::FoldTree const &f)
 
int residue_center_of_mass (conformation::Conformation const &conformation, int const start, int const stop)
 
int return_nearest_residue (conformation::Conformation const &conformation, int const begin, int const end, Vector center)
 
std::string show_foldtree (core::conformation::symmetry::SymmetricConformation const &symm_conf, SymmData const &symmdata, std::map< char, std::pair< Size, Size > > const &chain2range)
 
bool operator== (VirtualCoordinate const &a, VirtualCoordinate const &b)
 
bool operator!= (VirtualCoordinate const &a, VirtualCoordinate const &b)
 

Variables

static std::string const NOPARENT = "NOPARENT"
 

Typedef Documentation

typedef numeric::xyzMatrix<Real> core::conformation::symmetry::Mat

Definition at line 64 of file SymmData.cc.

typedef utility::pointer::owning_ptr< SymDof const > core::conformation::symmetry::SymDofCOP

Definition at line 24 of file SymDof.fwd.hh.

typedef utility::pointer::owning_ptr< SymDof > core::conformation::symmetry::SymDofOP

Definition at line 22 of file SymDof.fwd.hh.

typedef utility::pointer::owning_ptr< SymmData const > core::conformation::symmetry::SymmDataCOP

Definition at line 32 of file SymmData.fwd.hh.

typedef utility::pointer::owning_ptr< SymmDataLoader const > core::conformation::symmetry::SymmDataLoaderCOP

Definition at line 25 of file SymmDataLoader.fwd.hh.

typedef utility::pointer::owning_ptr< SymmDataLoader > core::conformation::symmetry::SymmDataLoaderOP

Definition at line 23 of file SymmDataLoader.fwd.hh.

typedef utility::pointer::owning_ptr< SymmData > core::conformation::symmetry::SymmDataOP

Definition at line 29 of file SymmData.fwd.hh.

typedef utility::pointer::owning_ptr< SymmDataOptions const > core::conformation::symmetry::SymmDataOptionsCOP

Definition at line 26 of file SymmDataOptions.fwd.hh.

typedef utility::pointer::owning_ptr< SymmDataOptions > core::conformation::symmetry::SymmDataOptionsOP

Definition at line 24 of file SymmDataOptions.fwd.hh.

typedef utility::pointer::owning_ptr< SymmetricConformation const > core::conformation::symmetry::SymmetricConformationCOP

Definition at line 24 of file SymmetricConformation.fwd.hh.

typedef utility::pointer::owning_ptr< SymmetricConformation > core::conformation::symmetry::SymmetricConformationOP

Definition at line 22 of file SymmetricConformation.fwd.hh.

typedef utility::pointer::owning_ptr< SymmetryInfo const > core::conformation::symmetry::SymmetryInfoCOP

Definition at line 24 of file SymmetryInfo.fwd.hh.

typedef utility::pointer::owning_ptr< SymmetryInfo > core::conformation::symmetry::SymmetryInfoOP

Definition at line 22 of file SymmetryInfo.fwd.hh.

typedef utility::pointer::owning_ptr< SymSlideInfo const > core::conformation::symmetry::SymSlideInfoCOP

Definition at line 24 of file SymSlideInfo.fwd.hh.

typedef utility::pointer::owning_ptr< SymSlideInfo > core::conformation::symmetry::SymSlideInfoOP

Definition at line 22 of file SymSlideInfo.fwd.hh.

typedef numeric::xyzVector<Real> core::conformation::symmetry::Vec

Definition at line 63 of file SymmData.cc.

typedef utility::pointer::owning_ptr< VirtualCoordinate const > core::conformation::symmetry::VirtualCoordinateCOP

Definition at line 24 of file VirtualCoordinate.fwd.hh.

typedef utility::pointer::owning_ptr< VirtualCoordinate > core::conformation::symmetry::VirtualCoordinateOP

Definition at line 22 of file VirtualCoordinate.fwd.hh.

typedef vector1< pair<Size,Real> > core::conformation::symmetry::WtedClones

Definition at line 68 of file SymmData.cc.

typedef numeric::xyzTransform<Real> core::conformation::symmetry::Xform

Definition at line 62 of file SymmData.cc.

Enumeration Type Documentation

enum core::conformation::symmetry::dof_type
Enumerator
X_DOF 
Y_DOF 
Z_DOF 
X_ANGLE_DOF 
Y_ANGLE_DOF 
Z_ANGLE_DOF 

Definition at line 37 of file SymDof.hh.

enum core::conformation::symmetry::SlideCriteriaType
Enumerator
CEN_DOCK_SCORE 
FA_REP_SCORE 
CONTACTS 
TOTAL_NUM_CRITERIA 

Definition at line 38 of file SymSlideInfo.hh.

enum core::conformation::symmetry::SlideType
Enumerator
SEQUENTIAL 
ORDERED_SEQUENTIAL 
RANDOM 

Definition at line 32 of file SymSlideInfo.hh.

Function Documentation

template<class T >
void core::conformation::symmetry::comma_strings_to_map ( std::istream &  is,
Size const  nbase,
std::map< Size, T > &  clones,
std::string  tag = "" 
)

Definition at line 420 of file SymmetryInfo.cc.

References protocols::forge::methods::replace(), and TR().

Referenced by operator>>().

void core::conformation::symmetry::comma_strings_to_map ( std::istream &  is,
Size const  nbase,
std::map< Size, SymDof > &  clones,
std::string  tag = "" 
)

Definition at line 459 of file SymmetryInfo.cc.

References protocols::forge::methods::replace(), and TR().

void core::conformation::symmetry::comma_strings_to_vector ( std::istream &  is,
Size const  nbase,
utility::vector1< Size > &  clones,
std::string  tag = "" 
)

Definition at line 501 of file SymmetryInfo.cc.

References protocols::forge::methods::replace(), and TR().

Referenced by operator>>().

template<class T >
void core::conformation::symmetry::comma_strings_to_vector_map ( std::istream &  is,
Size const  nbase,
std::map< Size, utility::vector1< T > > &  clones,
std::string  tag = "" 
)

Definition at line 370 of file SymmetryInfo.cc.

References protocols::forge::methods::replace(), core::io::serialization::size(), core::pack::interaction_graph::T(), and TR().

Referenced by operator>>().

Size core::conformation::symmetry::fold_tree_entry_point ( core::kinematics::FoldTree const &  ft,
Size  lb_resi = 0,
Size  ub_resi = 0 
)

Definition at line 65 of file util.cc.

References core::kinematics::FoldTree::downstream_jump_residue(), core::kinematics::FoldTree::nres(), core::kinematics::FoldTree::num_jump(), core::kinematics::FoldTree::root(), and core::kinematics::FoldTree::upstream_jump_residue().

Referenced by get_component_contiguous_foldtree(), and process_residue_request().

kinematics::FoldTree core::conformation::symmetry::get_asymm_unit_fold_tree ( core::conformation::Conformation const &  conf)

Definition at line 840 of file util.cc.

References core::kinematics::FoldTree::add_edge(), core::kinematics::FoldTree::begin(), core::kinematics::FoldTree::end(), core::conformation::Conformation::fold_tree(), is_symmetric(), core::kinematics::FoldTree::renumber_jumps(), core::kinematics::Edge::start(), and core::conformation::symmetry::SymmetricConformation::Symmetry_Info().

Referenced by core::conformation::symmetry::SymmetricConformation::append_residue_by_jump(), protocols::enzdes::DetectProteinLigandInterface::apply(), core::pose::symmetry::extract_asymmetric_unit(), core::conformation::symmetry::SymmetricConformation::fold_tree(), protocols::loops::fold_tree_from_loops(), protocols::hybridization::HybridizeFoldtreeDynamic::initialize(), core::conformation::symmetry::SymmetricConformation::insert_conformation_by_jump(), protocols::loops::set_single_loop_fold_tree(), and protocols::hybridization::HybridizeFoldtreeDynamic::update().

std::map<char,std::pair<Size,Size> > core::conformation::symmetry::get_chain2range ( Conformation const &  src_conf,
std::map< int, char >  src_conf2pdb_chain 
)

get a mapping of chain chars to resi ranges

Definition at line 186 of file util.cc.

References core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), and core::conformation::Conformation::num_chains().

Referenced by set_fold_tree_from_symm_data(), and setup_symmetric_conformation().

core::kinematics::FoldTree core::conformation::symmetry::get_component_contiguous_foldtree ( core::kinematics::FoldTree const &  f_orig,
std::map< char, std::pair< Size, Size > > const &   
)

Definition at line 116 of file util.cc.

References core::kinematics::FoldTree::cutpoint(), core::kinematics::FoldTree::downstream_atom(), fold_tree_entry_point(), core::kinematics::FoldTree::nres(), core::kinematics::FoldTree::num_cutpoint(), core::kinematics::FoldTree::num_jump(), core::kinematics::FoldTree::reorder(), core::kinematics::FoldTree::set_jump_atoms(), and core::kinematics::FoldTree::tree_from_jumps_and_cuts().

Referenced by setup_symmetric_conformation().

id::TorsionType core::conformation::symmetry::guess_torsion_type_of_dof_id ( id::DOF_ID const &  id,
Conformation const &  conf 
)

This is a helper function for some of the DOF_ID routines below. Really just a best guess... this is a little tricky: the mapping from a DOF_ID to a TorsionID is not straightforward to construct (see kinematics/util.cc:setup_dof_to_torsion_map) So we don't really know whether a dof_id is a bb degree of freedom or a chi degree of freedom... or even which residue it should be attached to, eg the phi of residue i might be dof_id with rsd i-1 So we take a guess based on whether id.atomno is a backbone or sidechain atom

Definition at line 254 of file SymmetryInfo.cc.

References core::conformation::Conformation::atom_is_backbone_norefold(), core::id::BB, core::id::CHI, core::id::JUMP, core::id::RB1, and core::id::RB6.

Referenced by core::conformation::symmetry::SymmetryInfo::dependent_dofs(), core::conformation::symmetry::SymmetryInfo::dof_is_independent(), and core::conformation::symmetry::SymmetryInfo::get_dof_derivative_weight().

bool core::conformation::symmetry::is_jump_intracomponent ( std::map< char, std::pair< Size, Size > >  chain2range,
Size  up,
Size  dn 
)

Definition at line 98 of file util.cc.

Referenced by set_fold_tree_from_symm_data().

bool core::conformation::symmetry::is_symmetric ( conformation::Conformation const &  conf)

Attempt to detect whether a conformation is symmetric

Definition at line 220 of file util.cc.

Referenced by core::optimization::symmetry::SymMinimizerMap::add_torsion(), protocols::topology_broker::FibrilModelingClaimer::allow_claim(), protocols::fldsgn::CircularPermutation::apply(), protocols::fldsgn::potentials::SetSecStructEnergies::apply(), protocols::topology_broker::TopologyBroker::apply(), core::pack::task::operation::RestrictToInterface::apply(), core::optimization::symmetry::atom_tree_dfunc(), core::optimization::symmetry::atom_tree_get_atompairE_deriv(), protocols::scoring::Interface::calculate(), core::optimization::cartesian_collect_atompairE_deriv(), core::optimization::cartesian_dfunc(), protocols::sasa_scores::compute_avge_scores(), core::scoring::methods::MetalloPlacementEnergy::finalize_total_energy(), get_asymm_unit_fold_tree(), core::pose::symmetry::is_symmetric(), core::optimization::symmetry::SymAtomTreeMinimizer::make_assymetric_movemap(), core::optimization::symmetry::SymAtomTreeMinimizer::make_semisymmetric_movemap(), protocols::simple_moves::symmetry::SymPackRotamersMover::make_symmetric_task(), protocols::features::DatabaseJobInputter::pose_from_job(), core::optimization::symmetry::SymAtomTreeMinimizer::run(), core::pose::symmetry::scorefxn_is_symmetric(), set_asymm_unit_fold_tree(), shift_jump_numbers_in_dofs(), protocols::topology_broker::TopologyBroker::switch_to_fullatom(), and symmetrize_fold_tree().

bool core::conformation::symmetry::is_symmetric ( conformation::symmetry::SymmetryInfo const &  symminfo)

Definition at line 226 of file util.cc.

References core::conformation::symmetry::SymmetryInfo::get_use_symmetry().

template<class CloneType >
void core::conformation::symmetry::map_to_comma_strings ( std::ostream &  out,
std::map< Size, CloneType >  clones,
std::string  tag = "" 
)

Definition at line 559 of file SymmetryInfo.cc.

Referenced by operator<<().

void core::conformation::symmetry::map_to_comma_strings ( std::ostream &  out,
std::map< Size, SymDof >  clones,
std::string  tag = "" 
)

Definition at line 573 of file SymmetryInfo.cc.

bool core::conformation::symmetry::operator!= ( SymSlideInfo const &  a,
SymSlideInfo const &  b 
)

Definition at line 119 of file SymSlideInfo.cc.

References protocols::match::upstream::b.

bool core::conformation::symmetry::operator!= ( VirtualCoordinate const &  a,
VirtualCoordinate const &  b 
)

Definition at line 144 of file VirtualCoordinate.cc.

References protocols::match::upstream::b.

bool core::conformation::symmetry::operator!= ( SymDof const &  a,
SymDof const &  b 
)

Definition at line 320 of file SymDof.cc.

References protocols::match::upstream::b.

std::ostream& core::conformation::symmetry::operator<< ( std::ostream &  s,
const SymDof &  dof 
)

Definition at line 270 of file SymDof.cc.

References core::conformation::symmetry::SymDof::allow_dof(), core::conformation::symmetry::SymDof::jump_direction(), core::conformation::symmetry::SymDof::range1_lower(), core::conformation::symmetry::SymDof::range1_upper(), core::conformation::symmetry::SymDof::range2_lower(), and core::conformation::symmetry::SymDof::range2_upper().

std::ostream& core::conformation::symmetry::operator<< ( std::ostream &  s,
const SymmetryInfo &  symminfo 
)

Definition at line 701 of file SymmetryInfo.cc.

References core::conformation::symmetry::SymmetryInfo::bb_clones_, core::conformation::symmetry::SymmetryInfo::bb_follows_, core::conformation::symmetry::SymmetryInfo::chi_clones_, core::conformation::symmetry::SymmetryInfo::chi_follows_, core::conformation::symmetry::SymmetryInfo::dofs_, core::conformation::symmetry::SymmetryInfo::jump_clone_wts_, core::conformation::symmetry::SymmetryInfo::jump_clones_, core::conformation::symmetry::SymmetryInfo::jump_follows_, map_to_comma_strings(), core::conformation::symmetry::SymmetryInfo::njump_monomer_, core::conformation::symmetry::SymmetryInfo::npseudo_, core::conformation::symmetry::SymmetryInfo::nres_monomer_, core::conformation::symmetry::SymmetryInfo::num_interfaces(), core::conformation::symmetry::SymmetryInfo::score_multiply_, core::conformation::symmetry::SymmetryInfo::scoring_subunit_, core::conformation::symmetry::SymmetryInfo::subunits(), core::conformation::symmetry::SymmetryInfo::type_, vector_map_to_comma_strings(), and vector_to_comma_strings().

bool core::conformation::symmetry::operator== ( SymSlideInfo const &  a,
SymSlideInfo const &  b 
)

Definition at line 106 of file SymSlideInfo.cc.

References core::conformation::symmetry::SymSlideInfo::score_criteria_, core::conformation::symmetry::SymSlideInfo::slide_order_, core::conformation::symmetry::SymSlideInfo::slide_type_, and core::conformation::symmetry::SymSlideInfo::SlideCriteriaVal_.

bool core::conformation::symmetry::operator== ( VirtualCoordinate const &  a,
VirtualCoordinate const &  b 
)

Definition at line 133 of file VirtualCoordinate.cc.

References core::conformation::symmetry::VirtualCoordinate::axis_origin_, core::conformation::symmetry::VirtualCoordinate::axis_x_, and core::conformation::symmetry::VirtualCoordinate::axis_y_.

bool core::conformation::symmetry::operator== ( SymDof const &  a,
SymDof const &  b 
)

Definition at line 302 of file SymDof.cc.

References core::conformation::symmetry::SymDof::allowed_dof_jumps_, core::conformation::symmetry::SymDof::has_range1_lower_, core::conformation::symmetry::SymDof::has_range1_upper_, core::conformation::symmetry::SymDof::has_range2_lower_, core::conformation::symmetry::SymDof::has_range2_upper_, core::conformation::symmetry::SymDof::jump_dir_, core::conformation::symmetry::SymDof::lower_range_dof_jumps1_, core::conformation::symmetry::SymDof::lower_range_dof_jumps2_, core::conformation::symmetry::SymDof::upper_range_dof_jumps1_, and core::conformation::symmetry::SymDof::upper_range_dof_jumps2_.

bool core::conformation::symmetry::operator== ( SymmData const &  a,
SymmData const &  b 
)

Definition at line 1645 of file SymmData.cc.

References core::conformation::symmetry::SymmData::allow_virtual_, core::conformation::symmetry::SymmData::anchor_residue_, core::conformation::symmetry::SymmData::cell_a_, core::conformation::symmetry::SymmData::cell_alfa_, core::conformation::symmetry::SymmData::cell_b_, core::conformation::symmetry::SymmData::cell_beta_, core::conformation::symmetry::SymmData::cell_c_, core::conformation::symmetry::SymmData::cell_gamma_, core::conformation::symmetry::SymmData::components_, core::conformation::symmetry::SymmData::dofs_, core::conformation::symmetry::SymmData::include_subunit_, core::conformation::symmetry::SymmData::interfaces_, core::conformation::symmetry::SymmData::jname2components_, core::conformation::symmetry::SymmData::jname2subunits_, core::conformation::symmetry::SymmData::jump_clones_, core::conformation::symmetry::SymmData::jump_string_to_jump_num_, core::conformation::symmetry::SymmData::jump_string_to_virtual_pair_, core::conformation::symmetry::SymmData::name2component_, core::conformation::symmetry::SymmData::num_components_, core::conformation::symmetry::SymmData::output_subunit_, core::conformation::symmetry::SymmData::recenter_, core::conformation::symmetry::SymmData::root_, core::conformation::symmetry::SymmData::rotation_matrices_, core::conformation::symmetry::SymmData::score_multiply_subunit_, core::conformation::symmetry::SymmData::score_subunit_, core::conformation::symmetry::SymmData::slide_info_, core::conformation::symmetry::SymmData::slide_order_string_, core::conformation::symmetry::SymmData::subunit_num_to_virt_id_, core::conformation::symmetry::SymmData::subunits_, core::conformation::symmetry::SymmData::symm_transforms_, core::conformation::symmetry::SymmData::symmetry_name_, core::conformation::symmetry::SymmData::symmetry_type_, core::conformation::symmetry::SymmData::translation_matrices_, core::conformation::symmetry::SymmData::virt_id_to_subunit_chain_, core::conformation::symmetry::SymmData::virt_id_to_subunit_num_, core::conformation::symmetry::SymmData::virt_id_to_subunit_residue_, core::conformation::symmetry::SymmData::virt_id_to_virt_num_, core::conformation::symmetry::SymmData::virt_num_to_virt_id_, and core::conformation::symmetry::SymmData::virtual_coordinates_.

std::istream& core::conformation::symmetry::operator>> ( std::istream &  s,
SymmetryInfo &  symminfo 
)

Definition at line 607 of file SymmetryInfo.cc.

References core::conformation::symmetry::SymmetryInfo::bb_clones_, core::conformation::symmetry::SymmetryInfo::bb_follows_, core::conformation::symmetry::SymmetryInfo::chi_clones_, core::conformation::symmetry::SymmetryInfo::chi_follows_, comma_strings_to_map(), comma_strings_to_vector(), comma_strings_to_vector_map(), core::conformation::symmetry::SymmetryInfo::dofs_, core::conformation::symmetry::SymmetryInfo::interfaces_, core::conformation::symmetry::SymmetryInfo::jump_clone_wts_, core::conformation::symmetry::SymmetryInfo::jump_clones_, core::conformation::symmetry::SymmetryInfo::jump_follows_, core::conformation::symmetry::SymmetryInfo::njump_monomer_, core::conformation::symmetry::SymmetryInfo::npseudo_, core::conformation::symmetry::SymmetryInfo::nres_monomer_, core::conformation::symmetry::SymmetryInfo::score_multiply_, core::conformation::symmetry::SymmetryInfo::scoring_subunit_, core::conformation::symmetry::SymmetryInfo::set_cp_weighting_during_minimization(), core::conformation::symmetry::SymmetryInfo::set_use_symmetry(), TR(), core::conformation::symmetry::SymmetryInfo::type_, and core::conformation::symmetry::SymmetryInfo::update_score_multiply_factor().

Size core::conformation::symmetry::process_residue_request ( conformation::Conformation const &  src_conf,
std::string  input,
Size  lb_resi = 0,
Size  ub_resi = 0 
)

get residue index

Definition at line 83 of file util.cc.

References core::conformation::Conformation::fold_tree(), fold_tree_entry_point(), residue_center_of_mass(), and core::conformation::Conformation::size().

Referenced by recenter(), and set_fold_tree_from_symm_data().

void core::conformation::symmetry::recenter ( conformation::Conformation &  src_conformation,
conformation::symmetry::SymmData &  symmdata 
)

Definition at line 796 of file util.cc.

References core::conformation::symmetry::SymmData::get_anchor_residue(), core::chemical::ResidueType::natoms(), process_residue_request(), core::conformation::Conformation::residue(), core::conformation::Conformation::residue_type(), core::conformation::Conformation::set_xyz(), core::conformation::Conformation::size(), trans(), and core::conformation::Conformation::xyz().

Referenced by setup_symmetric_conformation().

kinematics::FoldTree core::conformation::symmetry::replaced_symmetric_foldtree_with_new_monomer ( kinematics::FoldTree  symm_f,
conformation::symmetry::SymmetryInfo  symmetry_info,
kinematics::FoldTree  monomer_f 
)

Definition at line 765 of file util.cc.

References core::sequence::end, core::conformation::symmetry::SymmetryInfo::num_independent_residues(), and core::conformation::symmetry::SymmetryInfo::subunits().

Referenced by protocols::jumping::close_chainbreaks().

int core::conformation::symmetry::residue_center_of_mass ( conformation::Conformation const &  conformation,
int const  start,
int const  stop 
)

Definition at line 989 of file util.cc.

References core::conformation::Residue::atom(), core::conformation::Residue::is_protein(), core::conformation::Residue::nbr_atom_xyz(), core::conformation::Conformation::residue(), return_nearest_residue(), protocols::loops::stop, and core::conformation::Atom::xyz().

Referenced by protocols::protein_interface_design::movers::SetAtomTree::apply(), process_residue_request(), and protocols::flexpep_docking::FlexPepDockingFlags::setDefaultAnchors().

int core::conformation::symmetry::return_nearest_residue ( conformation::Conformation const &  conformation,
int const  begin,
int const  end,
Vector  center 
)

Definition at line 1014 of file util.cc.

References core::conformation::Residue::atom(), core::sequence::end, core::conformation::Residue::is_protein(), core::conformation::Residue::nbr_atom_xyz(), core::conformation::Conformation::residue(), and core::conformation::Atom::xyz().

Referenced by protocols::geometry::residue_center_of_mass(), residue_center_of_mass(), and protocols::flexpep_docking::FlexPepDockingFlags::setDefaultAnchors().

static numeric::random::RandomGenerator core::conformation::symmetry::RG ( 408529  )
static

Referenced by protocols::simple_moves::oop::OopRandomPuckMover::apply(), protocols::simple_moves::oop::OopRandomSmallMover::apply(), protocols::rigid::RollMover::apply(), protocols::loops::loop_closure::kinematic_closure::KinematicMover::apply(), protocols::swa::monte_carlo::RNA_TorsionMover::apply_random_nucleoside_torsion(), protocols::swa::monte_carlo::RNA_TorsionMover::apply_random_suite_torsion(), protocols::noesy_assign::FragsToAtomDist::compute_average_distances(), protocols::swa::monte_carlo::RNA_TorsionMover::crankshaft_alpha_gamma(), protocols::swa::monte_carlo::get_random_residue_at_chain_terminus(), protocols::geometry::random_reorientation_matrix(), protocols::swa::monte_carlo::RNA_TorsionMover::random_torsion_move(), protocols::protein_interface_design::PatchdockReader::read_patchdock(), protocols::hotspot_hashing::HotspotStubSet::remove_random_stubs_from_set(), protocols::swa::monte_carlo::RNA_TorsionMover::sample_near_nucleoside_torsion(), and protocols::swa::monte_carlo::RNA_TorsionMover::sample_near_suite_torsion().

void core::conformation::symmetry::set_asymm_unit_fold_tree ( core::conformation::Conformation &  conf,
kinematics::FoldTree const &  f 
)

Definition at line 975 of file util.cc.

References core::conformation::Conformation::fold_tree(), is_symmetric(), and symmetrize_fold_tree().

Referenced by core::pose::symmetry::set_asymm_unit_fold_tree().

kinematics::FoldTree core::conformation::symmetry::set_fold_tree_from_symm_data ( conformation::Conformation &  src_conformation,
conformation::symmetry::SymmData &  symmdata,
std::map< int, char >  src_conf2pdb_chain 
)

Definition at line 451 of file util.cc.

References core::conformation::Residue::atom_name(), core::kinematics::FoldTree::clear(), core::sequence::end, core::conformation::Conformation::fold_tree(), core::conformation::symmetry::SymmData::get_anchor_residue(), get_chain2range(), core::conformation::symmetry::SymmData::get_num_components(), core::conformation::symmetry::SymmData::get_subunits(), core::conformation::symmetry::SymmData::get_virt_id_to_subunit_chain(), core::conformation::symmetry::SymmData::get_virt_id_to_subunit_num(), core::conformation::symmetry::SymmData::get_virt_id_to_subunit_residue(), core::conformation::symmetry::SymmData::get_virtual_connects(), core::conformation::symmetry::SymmData::get_virtual_coordinates(), core::conformation::symmetry::SymmData::get_virtual_id_to_num(), core::conformation::symmetry::SymmData::get_virtual_num_to_id(), is_jump_intracomponent(), core::scoring::pair, process_residue_request(), core::conformation::Conformation::residue(), core::conformation::Conformation::size(), and TR().

Referenced by setup_symmetric_conformation().

conformation::symmetry::SymmetricConformationOP core::conformation::symmetry::setup_symmetric_conformation ( conformation::Conformation &  src_conformation,
conformation::symmetry::SymmData &  symmdata,
std::map< int, char >  src_conf2pdb_chain 
)

Generate a symmetric conformation from a monomeric pose and symmetry information stored in the SymmData object

Definition at line 259 of file util.cc.

References core::conformation::Conformation::append_residue_by_jump(), core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::conformation::symmetry::SymmData::components_moved_by_jump(), core::conformation::ResidueFactory::create_residue(), core::conformation::Conformation::fold_tree(), get_chain2range(), core::conformation::symmetry::SymmetryInfo::get_component_bounds(), get_component_contiguous_foldtree(), core::conformation::symmetry::SymmetryInfo::get_components(), core::conformation::symmetry::SymmData::get_components(), core::conformation::symmetry::SymmetryInfo::get_dofs(), core::conformation::symmetry::SymmetryInfo::get_jump_name(), core::conformation::symmetry::SymmData::get_jump_name_to_components(), core::conformation::symmetry::SymmData::get_jump_name_to_subunits(), core::conformation::symmetry::SymmData::get_num_components(), core::conformation::symmetry::SymmData::get_recenter(), core::conformation::symmetry::SymmData::get_root(), core::conformation::symmetry::SymmetryInfo::get_subunit_name_to_component(), core::conformation::symmetry::SymmData::get_subunit_name_to_component(), core::conformation::symmetry::SymmData::get_subunits(), core::conformation::symmetry::SymmData::get_virtual_connects(), core::conformation::symmetry::SymmData::get_virtual_coordinates(), core::conformation::symmetry::SymmData::get_virtual_num_to_id(), core::conformation::Conformation::insert_conformation_by_jump(), core::conformation::Conformation::jump(), core::conformation::symmetry::SymmetryInfo::jump_is_independent(), core::conformation::Conformation::num_chains(), core::kinematics::FoldTree::num_jump(), recenter(), core::conformation::Conformation::residue(), core::conformation::Residue::residue_type_set(), set_fold_tree_from_symm_data(), shift_jump_numbers_in_dofs(), show_foldtree(), core::conformation::Conformation::size(), core::conformation::symmetry::SymmData::subunits_moved_by_jump(), TR(), and core::kinematics::visualize_fold_tree().

Referenced by core::pose::symmetry::make_symmetric_pose().

void core::conformation::symmetry::shift_jump_numbers_in_dofs ( conformation::Conformation &  conformation,
Size  shift 
)

Definition at line 813 of file util.cc.

References is_symmetric(), and core::conformation::symmetry::SymmetricConformation::Symmetry_Info().

Referenced by setup_symmetric_conformation().

std::string core::conformation::symmetry::show_foldtree ( core::conformation::symmetry::SymmetricConformation const &  symm_conf,
SymmData const &  symmdata,
std::map< char, std::pair< Size, Size > > const &  chain2range 
)

Definition at line 1043 of file util.cc.

References core::conformation::symmetry::SymmetricConformation::fold_tree(), core::conformation::symmetry::SymmData::get_virtual_num_to_id(), core::conformation::symmetry::SymmetricConformation::Symmetry_Info(), and core::kinematics::visualize_fold_tree().

Referenced by setup_symmetric_conformation().

void core::conformation::symmetry::symmetrize_fold_tree ( core::conformation::Conformation const &  conf,
kinematics::FoldTree &  f 
)

Definition at line 870 of file util.cc.

References core::kinematics::FoldTree::clear(), core::kinematics::FoldTree::cutpoints(), core::kinematics::FoldTree::downstream_jump_residue(), core::conformation::Conformation::fold_tree(), is_symmetric(), core::kinematics::FoldTree::num_jump(), core::kinematics::FoldTree::root(), core::conformation::Conformation::size(), core::conformation::symmetry::SymmetricConformation::Symmetry_Info(), TR(), core::kinematics::FoldTree::tree_from_jumps_and_cuts(), and core::kinematics::FoldTree::upstream_jump_residue().

Referenced by core::conformation::symmetry::SymmetricConformation::append_residue_by_jump(), core::conformation::symmetry::SymmetricConformation::insert_conformation_by_jump(), set_asymm_unit_fold_tree(), and core::pose::symmetry::symmetrize_fold_tree().

static basic::Tracer core::conformation::symmetry::TR ( "core.conformation.symmetry.symmdatafactory"  )
static
static basic::Tracer core::conformation::symmetry::TR ( "core.conformation.symmetry.Conformation"  )
static
static basic::Tracer core::conformation::symmetry::TR ( "core.conformation.symmetry.util"  )
static
static basic::Tracer core::conformation::symmetry::TR ( "core.conformation.symmetry.SymmData"  )
static

Referenced by core::conformation::symmetry::SymmetricConformation::append_residue_by_jump(), core::conformation::symmetry::SymmetricConformation::batch_set_xyz(), comma_strings_to_map(), comma_strings_to_vector(), comma_strings_to_vector_map(), core::conformation::symmetry::SymmetricConformation::detect_disulfides(), core::conformation::symmetry::SymmetricConformation::insert_conformation_by_jump(), operator>>(), core::conformation::symmetry::SymmData::read_symmetry_data_from_stream(), core::conformation::symmetry::SymmetricConformation::replace_residue(), core::conformation::symmetry::SymmetricConformation::set_bond_angle(), core::conformation::symmetry::SymmetricConformation::set_bond_length(), core::conformation::symmetry::SymmetricConformation::set_dof(), set_fold_tree_from_symm_data(), core::conformation::symmetry::SymmetricConformation::set_jump(), core::conformation::symmetry::SymmetricConformation::set_jump_now(), core::conformation::symmetry::SymmetricConformation::set_secstruct(), core::conformation::symmetry::SymmetricConformation::set_torsion(), core::conformation::symmetry::SymmetricConformation::set_torsion_angle(), core::conformation::symmetry::SymmetricConformation::set_xyz(), setup_symmetric_conformation(), core::conformation::symmetry::SymmData::show(), symmetrize_fold_tree(), and core::conformation::symmetry::SymmetryInfo::SymmetryInfo().

template<class CloneType >
void core::conformation::symmetry::vector_map_to_comma_strings ( std::ostream &  out,
std::map< Size, utility::vector1< CloneType > >  clones,
std::string  tag = "" 
)

Definition at line 540 of file SymmetryInfo.cc.

Referenced by operator<<().

void core::conformation::symmetry::vector_to_comma_strings ( std::ostream &  out,
utility::vector1< Size >  clones,
std::string  tag = "" 
)

Definition at line 589 of file SymmetryInfo.cc.

Referenced by operator<<().

char core::conformation::symmetry::which_component ( std::map< char, std::pair< Size, Size > >  chain2range,
Size  resi 
)

Definition at line 106 of file util.cc.

Variable Documentation

std::string const core::conformation::symmetry::NOPARENT = "NOPARENT"
static

Definition at line 72 of file SymmData.cc.

Referenced by core::conformation::symmetry::SymmData::get_least_common_ancertor_jump(), core::conformation::symmetry::SymmData::get_least_common_ancertor_virtual(), core::conformation::symmetry::SymmData::get_parent_jump(), core::conformation::symmetry::SymmData::get_parent_virtual(), and core::conformation::symmetry::SymmData::is_ancestor_virtual().

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