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Rosetta
2016.11
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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 | SymmDataOptions |
class | SymmDataOptionsCreator |
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 |
typedef numeric::xyzTransform < Real > | Xform |
typedef numeric::xyzVector< Real > | Vec |
typedef numeric::xyzMatrix< Real > | Mat |
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 THREAD_LOCAL 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 THREAD_LOCAL basic::Tracer | TR ("core.conformation.symmetry.SymmData") |
bool | operator== (SymmData const &a, SymmData const &b) |
static THREAD_LOCAL 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 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 tag="") |
template<class S , class T > | |
void | comma_strings_to_map (std::istream &is, Size const nbase, std::map< S, T > &clones, std::string tag="") |
template<class S > | |
void | comma_strings_to_vector (std::istream &is, Size const nbase, utility::vector1< S > &clones, std::string tag="") |
void | comma_strings_to_map (std::istream &is, Size const nbase, std::map< Size, SymDof > &clones, std::string tag="") |
template<class S , class T > | |
void | vector_map_to_comma_strings (std::ostream &out, std::map< S, utility::vector1< T > > clones, std::string tag="") |
template<class S , class T > | |
void | map_to_comma_strings (std::ostream &out, std::map< S, T > clones, std::string 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 tag="") |
template<class S > | |
void | vector_to_comma_strings (std::ostream &out, utility::vector1< S > clones, std::string 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") |
static THREAD_LOCAL 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< int, 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< 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 numeric::xyzMatrix<Real> core::conformation::symmetry::Mat |
typedef utility::pointer::shared_ptr< MirrorSymmetricConformation const > core::conformation::symmetry::MirrorSymmetricConformationCOP |
typedef utility::pointer::shared_ptr< MirrorSymmetricConformation > core::conformation::symmetry::MirrorSymmetricConformationOP |
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< SymmetricConformation const > core::conformation::symmetry::SymmetricConformationCOP |
typedef utility::pointer::shared_ptr< SymmetricConformation > core::conformation::symmetry::SymmetricConformationOP |
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< SymmetryTransform > core::conformation::symmetry::SymmetryTransformOP |
typedef utility::pointer::shared_ptr< SymSlideInfo const > core::conformation::symmetry::SymSlideInfoCOP |
typedef utility::pointer::shared_ptr< SymSlideInfo > core::conformation::symmetry::SymSlideInfoOP |
typedef numeric::xyzVector<Real> core::conformation::symmetry::Vec |
typedef utility::pointer::shared_ptr< VirtualCoordinate const > core::conformation::symmetry::VirtualCoordinateCOP |
typedef utility::pointer::shared_ptr< VirtualCoordinate > core::conformation::symmetry::VirtualCoordinateOP |
typedef vector1< pair<Size,Real> > core::conformation::symmetry::WtedClones |
typedef numeric::xyzTransform<Real> core::conformation::symmetry::Xform |
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::kinematics::FoldTree::begin(), core::kinematics::FoldTree::end(), 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().
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static |
Referenced by get_chain2range().
void core::conformation::symmetry::comma_strings_to_map | ( | std::istream & | is, |
Size const | nbase, | ||
std::map< S, T > & | clones, | ||
std::string | 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 | tag = "" |
||
) |
References protocols::forge::methods::replace(), and TR().
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 | tag = "" |
||
) |
helper function for symminfo serialization
References protocols::forge::methods::replace(), core::chemical::element::S, TR(), and core::chemical::element::U.
Referenced by operator>>().
void core::conformation::symmetry::comma_strings_to_vector | ( | std::istream & | is, |
Size const | nbase, | ||
utility::vector1< S > & | clones, | ||
std::string | 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_vector_map | ( | std::istream & | is, |
Size const | nbase, | ||
std::map< S, utility::vector1< T > > & | clones, | ||
std::string | 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 |
||
) |
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 | ) |
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(), protocols::cryst::MakeLatticeMover::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::MirrorSymmetricConformation::insert_conformation_by_jump(), core::conformation::symmetry::SymmetricConformation::insert_conformation_by_jump(), protocols::rbsegment_relax::setup_disconnected(), protocols::rbsegment_relax::setup_pose_rbsegs_keep_loops(), 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
References core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), chr_chains(), 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 & | |||
) |
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
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 | ||
) |
Referenced by set_fold_tree_from_symm_data().
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::toolbox::task_operations::SelectByDeltaScoreOperation::apply(), protocols::toolbox::task_operations::CrystalContactsOperation::apply(), protocols::symmetric_docking::membrane::MPSymDockMover::apply(), protocols::fldsgn::CircularPermutation::apply(), protocols::fldsgn::potentials::SetSecStructEnergies::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::scoring::Interface::calculate(), core::optimization::cartesian_collect_atompairE_deriv(), core::optimization::cartesian_dfunc(), core::optimization::symmetry::SymAtomTreeMinimizer::check_and_correct_edge_weights_for_new_minimizer(), protocols::simple_filters::GeometryFilter::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(), protocols::loop_modeling::utilities::PrepareForFullatom::do_apply(), protocols::loop_modeling::refiners::MinimizationRefiner::do_apply(), core::scoring::electron_density::FastDensEnergy::eval_residue_pair_derivatives(), get_asymm_unit_fold_tree(), core::pose::symmetry::is_symmetric(), core::optimization::symmetry::SymAtomTreeMinimizer::make_asymmetric_movemap(), core::optimization::symmetry::SymAtomTreeMinimizer::make_semisymmetric_movemap(), protocols::simple_moves::symmetry::SymPackRotamersMover::make_symmetric_task(), protocols::features::DatabaseJobInputter::pose_from_job(), protocols::denovo_design::DisulfidizeMover::process_pose(), core::optimization::symmetry::SymAtomTreeMinimizer::run(), core::pose::symmetry::scorefxn_is_symmetric(), set_asymm_unit_fold_tree(), shift_jump_numbers_in_dofs(), protocols::forge::remodel::RemodelLoopMover::simultaneous_stage(), protocols::topology_broker::TopologyBroker::switch_to_fullatom(), and symmetrize_fold_tree().
bool core::conformation::symmetry::is_symmetric | ( | conformation::symmetry::SymmetryInfo const & | symminfo | ) |
void core::conformation::symmetry::map_to_comma_strings | ( | std::ostream & | out, |
std::map< S, T > | clones, | ||
std::string | tag = "" |
||
) |
helper function for symminfo serialization
Referenced by operator<<().
bool core::conformation::symmetry::operator!= | ( | SymSlideInfo const & | a, |
SymSlideInfo const & | b | ||
) |
References protocols::match::upstream::b.
bool core::conformation::symmetry::operator!= | ( | VirtualCoordinate const & | a, |
VirtualCoordinate const & | b | ||
) |
References protocols::match::upstream::b.
bool core::conformation::symmetry::operator!= | ( | SymDof const & | a, |
SymDof const & | b | ||
) |
References protocols::match::upstream::b.
std::ostream& core::conformation::symmetry::operator<< | ( | std::ostream & | s, |
const SymDof & | dof | ||
) |
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 | ||
) |
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 | ||
) |
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 | ||
) |
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().
void core::conformation::symmetry::pair_map_to_comma_strings | ( | std::ostream & | out, |
std::map< S, std::pair< T, U > > | clones, | ||
std::string | 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 , |
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Size | ub_resi = 0 |
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) |
get residue index
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 | ||
) |
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 | ||
) |
int core::conformation::symmetry::residue_center_of_mass | ( | conformation::Conformation const & | conformation, |
int const | start, | ||
int const | stop | ||
) |
References core::conformation::Residue::atom(), core::conformation::membrane::center, 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(), protocols::relax::RangeRelaxMover::finalize_setup(), process_residue_request(), and protocols::relax::membrane::MPFastRelaxMover::setup_relax_foldtree().
int core::conformation::symmetry::return_nearest_residue | ( | conformation::Conformation const & | conformation, |
int const | begin, | ||
int const | end, | ||
Vector | center | ||
) |
References core::conformation::Residue::atom(), core::conformation::membrane::center, 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 residue_center_of_mass().
void core::conformation::symmetry::set_asymm_unit_fold_tree | ( | core::conformation::Conformation & | conf, |
kinematics::FoldTree const & | f | ||
) |
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 | ||
) |
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(), core::chemical::element::I, 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
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::simple_filters::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::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 | ||
) |
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 | ||
) |
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 | ||
) |
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(), protocols::cryst::MakeLatticeMover::apply(), core::conformation::symmetry::MirrorSymmetricConformation::insert_conformation_by_jump(), core::conformation::symmetry::SymmetricConformation::insert_conformation_by_jump(), set_asymm_unit_fold_tree(), and core::pose::symmetry::symmetrize_fold_tree().
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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(), and core::conformation::symmetry::SymmetryInfo::SymmetryInfo().
void core::conformation::symmetry::vector_map_to_comma_strings | ( | std::ostream & | out, |
std::map< S, utility::vector1< T > > | clones, | ||
std::string | tag = "" |
||
) |
helper function for symminfo serialization
Referenced by operator<<().
void core::conformation::symmetry::vector_to_comma_strings | ( | std::ostream & | out, |
utility::vector1< S > | clones, | ||
std::string | 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 | ||
) |
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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().