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core::conformation::symmetry Namespace Reference

Classes

class  MirrorSymmetricConformation
 Mirror symmetric conformation contains the same symminfo logic, but also includes special logic for mirror symmetries. More...
 
class  SymDof
 
class  SymmData
 
class  SymmDataLoader
 
class  SymmDataLoaderCreator
 
class  SymmetricConformation
 A symmetric conformation: has an additional data member "SymmetryInfo" class. More...
 
class  SymmetryInfo
 
class  SymmetryTransform
 
class  SymSlideInfo
 
class  VirtualCoordinate
 

Typedefs

typedef
utility::pointer::shared_ptr
< MirrorSymmetricConformation
MirrorSymmetricConformationOP
 
typedef
utility::pointer::shared_ptr
< MirrorSymmetricConformation
const > 
MirrorSymmetricConformationCOP
 
typedef
utility::pointer::shared_ptr
< SymDof
SymDofOP
 
typedef
utility::pointer::shared_ptr
< SymDof const > 
SymDofCOP
 
using Xform = numeric::xyzTransform< Real >
 
using Vec = numeric::xyzVector< Real >
 
using Mat = numeric::xyzMatrix< Real >
 
typedef vector1< pair< Size,
Real > > 
WtedClones
 
typedef
utility::pointer::shared_ptr
< SymmData
SymmDataOP
 
typedef
utility::pointer::shared_ptr
< SymmData const > 
SymmDataCOP
 
typedef
utility::pointer::shared_ptr
< SymmDataLoader
SymmDataLoaderOP
 
typedef
utility::pointer::shared_ptr
< SymmDataLoader const > 
SymmDataLoaderCOP
 
typedef
utility::pointer::shared_ptr
< SymmDataOptions > 
SymmDataOptionsOP
 
typedef
utility::pointer::shared_ptr
< SymmDataOptions const > 
SymmDataOptionsCOP
 
typedef
utility::pointer::shared_ptr
< SymmetricConformation
SymmetricConformationOP
 
typedef
utility::pointer::shared_ptr
< SymmetricConformation const > 
SymmetricConformationCOP
 
typedef
utility::pointer::shared_ptr
< SymmetryInfo
SymmetryInfoOP
 
typedef
utility::pointer::shared_ptr
< SymmetryInfo const > 
SymmetryInfoCOP
 
typedef
utility::pointer::shared_ptr
< SymmetryTransform
SymmetryTransformOP
 
typedef
utility::pointer::shared_ptr
< SymmetryTransform const > 
SymmetryTransformCOP
 
typedef
utility::pointer::shared_ptr
< SymSlideInfo
SymSlideInfoOP
 
typedef
utility::pointer::shared_ptr
< SymSlideInfo const > 
SymSlideInfoCOP
 
typedef
utility::pointer::shared_ptr
< VirtualCoordinate
VirtualCoordinateOP
 
typedef
utility::pointer::shared_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

static basic::Tracer TR ("core.conformation.symmetry.Conformation")
 
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.Conformation")
 
template<class S , class T >
void comma_strings_to_vector_map (std::istream &is, Size const nbase, std::map< S, utility::vector1< T > > &clones, std::string const &tag="")
 
template<class S , class T , class U >
void comma_strings_to_pair_map (std::istream &is, Size const nbase, std::map< S, std::pair< T, U > > &clones, std::string const &tag="")
 
template<class S , class T >
void comma_strings_to_map (std::istream &is, Size const nbase, std::map< S, T > &clones, std::string const &tag="")
 
template<class S >
void comma_strings_to_vector (std::istream &is, Size const nbase, utility::vector1< S > &clones, std::string const &tag="")
 
void comma_strings_to_map (std::istream &is, Size const nbase, std::map< Size, SymDof > &clones, std::string const &tag="")
 
template<class S , class T >
void vector_map_to_comma_strings (std::ostream &out, std::map< S, utility::vector1< T > > clones, std::string const &tag="")
 
template<class S , class T >
void map_to_comma_strings (std::ostream &out, std::map< S, T > clones, std::string const &tag="")
 
template<class S , class T , class U >
void pair_map_to_comma_strings (std::ostream &out, std::map< S, std::pair< T, U > > clones, std::string const &tag="")
 
template<class S >
void vector_to_comma_strings (std::ostream &out, utility::vector1< S > clones, std::string const &tag="")
 
id::TorsionType guess_torsion_type_of_dof_id (id::DOF_ID const &id, Conformation const &conf)
 
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 std::string const chr_chains ("ABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789!@#$&.<>?]{}|-_\\~=%zyxwvutsrqponmlkjihgfedcbaABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789!@#$&.<>?]{}|-_\\~=%zyxwvutsrqponmlkjihgfedcbaABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789!@#$&.<>?]{}|-_\\~=%zyxwvutsrqponmlkjihgfedcbaABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789!@#$&.<>?]{}|-_\\~=%zyxwvutsrqponmlkjihgfedcbaABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789!@#$&.<>?]{}|-_\\~=%zyxwvutsrqponmlkjihgfedcbaABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789!@#$&.<>?]{}|-_\\~=%zyxwvutsrqponmlkjihgfedcbaABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789!@#$&.<>?]{}|-_\\~=%zyxwvutsrqponmlkjihgfedcbaABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789!@#$&.<>?]{}|-_\\~=%zyxwvutsrqponmlkjihgfedcba")
 
std::string get_chain_id_string ()
 
static basic::Tracer TR ("core.conformation.symmetry.util")
 
void calculate_inverting_virtuals (core::kinematics::FoldTree const &ft, Conformation const &conf, SymmetryInfo const &symm_info, utility::vector1< bool > &mirrored_subs, utility::vector1< std::pair< bool, bool > > &mirrored_jumps)
 A very specific helper function that counts the number of mirror ops from root->each subunit More...
 
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< core::Size, char > src_conf2pdb_chain)
 
bool is_symmetric (conformation::Conformation const &conf)
 
bool is_mirror_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< core::Size, char > src_conf2pdb_chain)
 
kinematics::FoldTree set_fold_tree_from_symm_data (conformation::Conformation &src_conformation, conformation::symmetry::SymmData &symmdata, std::map< core::Size, 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)
 Converts an asymmetric foldtree (f) with virtual root into a symmetric foldtree compatible with symmetric conformation (conf) More...
 
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

using core::conformation::symmetry::Mat = typedef numeric::xyzMatrix<Real>
typedef utility::pointer::shared_ptr< SymDof const > core::conformation::symmetry::SymDofCOP
typedef utility::pointer::shared_ptr< SymDof > core::conformation::symmetry::SymDofOP
typedef utility::pointer::shared_ptr< SymmData const > core::conformation::symmetry::SymmDataCOP
typedef utility::pointer::shared_ptr< SymmDataLoader const > core::conformation::symmetry::SymmDataLoaderCOP
typedef utility::pointer::shared_ptr< SymmDataLoader > core::conformation::symmetry::SymmDataLoaderOP
typedef utility::pointer::shared_ptr< SymmData > core::conformation::symmetry::SymmDataOP
typedef utility::pointer::shared_ptr< SymmDataOptions const > core::conformation::symmetry::SymmDataOptionsCOP
typedef utility::pointer::shared_ptr< SymmDataOptions > core::conformation::symmetry::SymmDataOptionsOP
typedef utility::pointer::shared_ptr< SymmetryInfo const > core::conformation::symmetry::SymmetryInfoCOP
typedef utility::pointer::shared_ptr< SymmetryInfo > core::conformation::symmetry::SymmetryInfoOP
typedef utility::pointer::shared_ptr< SymmetryTransform const > core::conformation::symmetry::SymmetryTransformCOP
typedef utility::pointer::shared_ptr< SymSlideInfo const > core::conformation::symmetry::SymSlideInfoCOP
typedef utility::pointer::shared_ptr< SymSlideInfo > core::conformation::symmetry::SymSlideInfoOP
using core::conformation::symmetry::Vec = typedef numeric::xyzVector<Real>
typedef utility::pointer::shared_ptr< VirtualCoordinate const > core::conformation::symmetry::VirtualCoordinateCOP
using core::conformation::symmetry::Xform = typedef numeric::xyzTransform<Real>

Enumeration Type Documentation

Enumerator
X_DOF 
Y_DOF 
Z_DOF 
X_ANGLE_DOF 
Y_ANGLE_DOF 
Z_ANGLE_DOF 
Enumerator
CEN_DOCK_SCORE 
FA_REP_SCORE 
CONTACTS 
TOTAL_NUM_CRITERIA 
Enumerator
SEQUENTIAL 
ORDERED_SEQUENTIAL 
RANDOM 

Function Documentation

void core::conformation::symmetry::calculate_inverting_virtuals ( core::kinematics::FoldTree const &  ft,
Conformation const &  conf,
SymmetryInfo const &  symm_info,
utility::vector1< bool > &  mirrored_subs,
utility::vector1< std::pair< bool, bool > > &  inverted_jumps 
)

A very specific helper function that counts the number of mirror ops from root->each subunit

A very specific helper function that counts the number of mirror ops from root->each subunit returns: a bool vector 'mirrored_subs' that defines which subunits are mirrored w.r.t. master a bool pair vector 'mirrored_jumps' that defines which jumps are mirrored w.r.t. master (upstream/downstream)

References core::chemical::ResidueType::is_inverted_virtual_residue(), core::conformation::symmetry::SymmetryInfo::num_total_residues_without_pseudo(), core::conformation::Conformation::residue_type(), and core::conformation::symmetry::SymmetryInfo::subunit_index().

Referenced by core::conformation::symmetry::MirrorSymmetricConformation::update_njumps_nres().

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

helper function for symminfo serialization

References protocols::forge::methods::replace(), core::chemical::element::S, 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 const &  tag = "" 
)
template<class S , class T , class U >
void core::conformation::symmetry::comma_strings_to_pair_map ( std::istream &  is,
Size const  nbase,
std::map< S, std::pair< T, U > > &  clones,
std::string const &  tag = "" 
)

helper function for symminfo serialization

References protocols::forge::methods::replace(), core::chemical::element::S, TR(), and core::chemical::element::U.

Referenced by operator>>().

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

helper function for symminfo serialization

References protocols::forge::methods::replace(), core::chemical::element::S, and TR().

Referenced by operator>>().

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

helper function for symminfo serialization

References protocols::forge::methods::replace(), core::chemical::element::S, 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 
)
kinematics::FoldTree core::conformation::symmetry::get_asymm_unit_fold_tree ( core::conformation::Conformation const &  conf)
std::map<char,std::pair<Size,Size> > core::conformation::symmetry::get_chain2range ( Conformation const &  src_conf,
std::map< core::Size, char >  src_conf2pdb_chain 
)
std::string core::conformation::symmetry::get_chain_id_string ( )

References chr_chains().

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

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

Attempt to detect whether a conformation is mirror symmetric

Referenced by protocols::cryst::MakeLatticeMover::apply(), and core::pose::symmetry::is_mirror_symmetric().

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

Attempt to detect whether a conformation is symmetric

Referenced by core::optimization::symmetry::SymMinimizerMap::add_torsion(), protocols::forge::remodel::RemodelGlobalFrame::align_segment(), protocols::topology_broker::FibrilModelingClaimer::allow_claim(), protocols::matdes::MotifHitsRotamersOperation::alter_rotamer_set(), protocols::task_operations::SelectByDeltaScoreOperation::apply(), protocols::task_operations::CrystalContactsOperation::apply(), protocols::cyclic_peptide::CrosslinkerMover::apply(), protocols::symmetric_docking::membrane::MPSymDockMover::apply(), protocols::fldsgn::CircularPermutation::apply(), protocols::topology_broker::TopologyBroker::apply(), protocols::forge::remodel::RemodelLoopMover::apply(), core::optimization::symmetry::atom_tree_dfunc(), core::optimization::symmetry::atom_tree_get_atompairE_deriv(), protocols::analysis::burial_metrics::PolarGroupBurialPyMolStringMetric::calculate(), core::simple_metrics::per_residue_metrics::PerResidueRMSDMetric::calculate(), core::simple_metrics::metrics::RMSDMetric::calculate(), protocols::scoring::Interface::calculate(), core::optimization::cartesian_collect_atompairE_deriv(), core::optimization::cartesian_dfunc(), protocols::score_filters::GeometryFilter::compute(), protocols::simple_filters::BuriedUnsatHbondFilter::compute(), protocols::matdes::SymUnsatHbondFilter::compute(), protocols::sasa_scores::compute_avge_scores(), protocols::forge::remodel::RemodelMover::design_refine_cart_relax(), protocols::forge::remodel::RemodelMover::design_refine_seq_relax(), core::scoring::electron_density::FastDensEnergy::eval_residue_pair_derivatives(), protocols::pose_creation::MergePDBMover::generate_overlaps(), get_asymm_unit_fold_tree(), protocols::fldsgn::potentials::SetSecStructEnergies::get_secstruct(), core::scoring::nmr::pre::PRESingleSet::init_from_filedata(), core::scoring::nmr::pcs::PCSSingleSet::init_from_pcs_filedata(), core::scoring::nmr::pre::PREMultiSet::init_from_pre_singleset_vec(), core::scoring::nmr::rdc::RDCSingleSet::init_from_rdc_filedata(), core::scoring::nmr::rdc::RDCMultiSet::init_from_rdc_filedata(), core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::initialize_graph_for_packing(), core::pose::symmetry::is_symmetric(), core::optimization::symmetry::SymAtomTreeMinimizer::make_asymmetric_movemap(), core::optimization::symmetry::SymAtomTreeMinimizer::make_semisymmetric_movemap(), protocols::features::DatabaseJobInputter::pose_from_job(), protocols::denovo_design::DisulfidizeMover::process_pose(), core::optimization::symmetry::SymAtomTreeMinimizer::run(), core::optimization::CartesianMinimizer::run(), core::pose::symmetry::scorefxn_is_symmetric(), set_asymm_unit_fold_tree(), core::scoring::nmr::pcs::PCSSingleSet::set_atom_derivatives(), core::scoring::nmr::rdc::RDCMultiSet::set_atom_derivatives(), core::scoring::nmr::pre::PREMultiSet::set_atom_derivatives(), protocols::relax::RepeatProteinRelax::setup_repeat_pose(), protocols::relax::RepeatProteinRelax::setup_repeat_pose_jumping(), shift_jump_numbers_in_dofs(), protocols::forge::remodel::RemodelLoopMover::simultaneous_stage(), core::scoring::superimpose_pose(), protocols::topology_broker::TopologyBroker::switch_to_fullatom(), symmetrize_fold_tree(), core::scoring::nmr::pcs::PCSSingleSet::update_spin_coordinates(), core::scoring::nmr::rdc::RDCMultiSet::update_spin_coordinates(), and core::scoring::nmr::pre::PREMultiSet::update_spin_coordinates().

bool core::conformation::symmetry::is_symmetric ( conformation::symmetry::SymmetryInfo const &  symminfo)
template<class S , class T >
void core::conformation::symmetry::map_to_comma_strings ( std::ostream &  out,
std::map< S, T >  clones,
std::string const &  tag = "" 
)

helper function for symminfo serialization

Referenced by operator<<().

bool core::conformation::symmetry::operator!= ( SymSlideInfo const &  a,
SymSlideInfo const &  b 
)
bool core::conformation::symmetry::operator!= ( VirtualCoordinate const &  a,
VirtualCoordinate const &  b 
)
bool core::conformation::symmetry::operator!= ( SymDof const &  a,
SymDof const &  b 
)
std::ostream& core::conformation::symmetry::operator<< ( std::ostream &  s,
const SymDof &  dof 
)
std::ostream& core::conformation::symmetry::operator<< ( std::ostream &  s,
const SymmetryInfo &  symminfo 
)

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::component_bounds_, core::conformation::symmetry::SymmetryInfo::components_, core::conformation::symmetry::SymmetryInfo::dofname2jnum_, core::conformation::symmetry::SymmetryInfo::dofs_, core::conformation::symmetry::SymmetryInfo::jname2components_, core::conformation::symmetry::SymmetryInfo::jname2subunits_, core::conformation::symmetry::SymmetryInfo::jnum2dofname_, 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::name2component_, core::conformation::symmetry::SymmetryInfo::njump_monomer_, core::conformation::symmetry::SymmetryInfo::npseudo_, core::conformation::symmetry::SymmetryInfo::nres_monomer_, core::conformation::symmetry::SymmetryInfo::num_components_, core::conformation::symmetry::SymmetryInfo::num_interfaces(), pair_map_to_comma_strings(), 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 
)
bool core::conformation::symmetry::operator== ( VirtualCoordinate const &  a,
VirtualCoordinate const &  b 
)
bool core::conformation::symmetry::operator== ( SymDof const &  a,
SymDof const &  b 
)
bool core::conformation::symmetry::operator== ( SymmData const &  a,
SymmData const &  b 
)

References core::conformation::symmetry::SymmData::allow_virtual_, core::conformation::symmetry::SymmData::anchor_residue_, 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 
)

References core::conformation::symmetry::SymmetryInfo::bb_clones_, core::conformation::symmetry::SymmetryInfo::bb_follows_, core::conformation::symmetry::SymmetryInfo::bb_is_independent(), core::conformation::symmetry::SymmetryInfo::chi_clones_, core::conformation::symmetry::SymmetryInfo::chi_follows_, comma_strings_to_map(), comma_strings_to_pair_map(), comma_strings_to_vector(), comma_strings_to_vector_map(), core::conformation::symmetry::SymmetryInfo::component_bounds_, core::conformation::symmetry::SymmetryInfo::components_, core::conformation::symmetry::SymmetryInfo::dofname2jnum_, core::conformation::symmetry::SymmetryInfo::dofs_, core::conformation::symmetry::SymmetryInfo::interfaces_, core::conformation::symmetry::SymmetryInfo::jname2components_, core::conformation::symmetry::SymmetryInfo::jname2subunits_, core::conformation::symmetry::SymmetryInfo::jnum2dofname_, core::conformation::symmetry::SymmetryInfo::jump_clone_wts_, core::conformation::symmetry::SymmetryInfo::jump_clones_, core::conformation::symmetry::SymmetryInfo::jump_follows_, core::conformation::symmetry::SymmetryInfo::last_indep_residue_, core::conformation::symmetry::SymmetryInfo::name2component_, core::conformation::symmetry::SymmetryInfo::njump_monomer_, core::conformation::symmetry::SymmetryInfo::npseudo_, core::conformation::symmetry::SymmetryInfo::nres_monomer_, core::conformation::symmetry::SymmetryInfo::num_components_, core::conformation::symmetry::SymmetryInfo::num_total_residues_without_pseudo(), core::conformation::symmetry::SymmetryInfo::score_multiply_, core::conformation::symmetry::SymmetryInfo::scoring_subunit_, core::conformation::symmetry::SymmetryInfo::set_use_symmetry(), TR(), core::conformation::symmetry::SymmetryInfo::type_, and core::conformation::symmetry::SymmetryInfo::update_score_multiply_factor().

template<class S , class T , class U >
void core::conformation::symmetry::pair_map_to_comma_strings ( std::ostream &  out,
std::map< S, std::pair< T, U > >  clones,
std::string const &  tag = "" 
)

helper function for symminfo serialization

Referenced by operator<<().

Size core::conformation::symmetry::process_residue_request ( conformation::Conformation const &  src_conf,
std::string  input,
Size  lb_resi = 0,
Size  ub_resi = 0 
)
void core::conformation::symmetry::recenter ( conformation::Conformation &  src_conformation,
conformation::symmetry::SymmData &  symmdata 
)
kinematics::FoldTree core::conformation::symmetry::replaced_symmetric_foldtree_with_new_monomer ( kinematics::FoldTree  symm_f,
conformation::symmetry::SymmetryInfo  symmetry_info,
kinematics::FoldTree  monomer_f 
)
int core::conformation::symmetry::residue_center_of_mass ( conformation::Conformation const &  conformation,
int const  start,
int const  stop 
)
int core::conformation::symmetry::return_nearest_residue ( conformation::Conformation const &  conformation,
int const  begin,
int const  end,
Vector  center 
)
void core::conformation::symmetry::set_asymm_unit_fold_tree ( core::conformation::Conformation conf,
kinematics::FoldTree const &  f 
)
kinematics::FoldTree core::conformation::symmetry::set_fold_tree_from_symm_data ( conformation::Conformation &  src_conformation,
conformation::symmetry::SymmData &  symmdata,
std::map< core::Size, char >  src_conf2pdb_chain 
)
conformation::symmetry::SymmetricConformationOP core::conformation::symmetry::setup_symmetric_conformation ( conformation::Conformation &  src_conformation,
conformation::symmetry::SymmData &  symmdata,
std::map< core::Size, char >  src_conf2pdb_chain 
)

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

References core::conformation::Conformation::append_residue_by_jump(), core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::conformation::Conformation::clone(), core::conformation::symmetry::SymmData::components_moved_by_jump(), protocols::splice::coords(), 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::SymmData::get_components(), core::conformation::symmetry::SymmetryInfo::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::SymmData::get_subunit_name_to_component(), core::conformation::symmetry::SymmetryInfo::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::inv_virtual_type_for_conf(), 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_type_set_for_conf(), 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(), core::conformation::virtual_type_for_conf(), 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 
)
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 
)
void core::conformation::symmetry::symmetrize_fold_tree ( core::conformation::Conformation const &  conf,
kinematics::FoldTree &  f 
)

Converts an asymmetric foldtree (f) with virtual root into a symmetric foldtree compatible with symmetric conformation (conf)

Parameters
conf- A symmetric conformation
f- An asymmetric foldtree. This foldtree MUST have a virtual root

This function does not require the symm data

References core::kinematics::FoldTree::clear(), core::kinematics::FoldTree::cutpoints(), core::kinematics::FoldTree::downstream_jump_residue(), core::conformation::Conformation::fold_tree(), is_symmetric(), protocols::mean_field::max(), protocols::mean_field::min(), 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_polymer_residue_after_seqpos(), core::conformation::symmetry::SymmetricConformation::append_residue_by_jump(), protocols::cryst::MakeLayerMover::apply(), protocols::cryst::MakeLatticeMover::apply(), protocols::loop_grower::LoopGrower::apply(), core::conformation::symmetry::MirrorSymmetricConformation::insert_conformation_by_jump(), core::conformation::symmetry::SymmetricConformation::insert_conformation_by_jump(), core::conformation::symmetry::SymmetricConformation::prepend_polymer_residue_before_seqpos(), set_asymm_unit_fold_tree(), and core::pose::symmetry::symmetrize_fold_tree().

static basic::Tracer core::conformation::symmetry::TR ( "core.conformation.symmetry.util"  )
static
static basic::Tracer core::conformation::symmetry::TR ( "core.conformation.symmetry.SymmData"  )
static
static basic::Tracer core::conformation::symmetry::TR ( "core.conformation.symmetry.Conformation"  )
static
static basic::Tracer core::conformation::symmetry::TR ( "core.conformation.symmetry.Conformation"  )
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_pair_map(), comma_strings_to_vector(), comma_strings_to_vector_map(), core::conformation::symmetry::SymmetricConformation::declare_chemical_bond(), 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_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(), core::conformation::symmetry::SymmetryInfo::SymmetryInfo(), and core::conformation::symmetry::SymmetricConformation::update_noncanonical_connection().

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

helper function for symminfo serialization

Referenced by operator<<().

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

helper function for symminfo serialization

Referenced by operator<<().

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

Variable Documentation

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