Rosetta 3.4
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core::conformation::symmetry Namespace Reference

Classes

class  SymDof
class  SymmData
class  SymmDataFactory
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 utility::vector1
< std::pair< Size, Real > > 
WtedClones
typedef
utility::pointer::owning_ptr
< SymmData
SymmDataOP
typedef
utility::pointer::owning_ptr
< SymmData const > 
SymmDataCOP
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)
static basic::Tracer TR ("core.conformation.symmetry.SymmData")
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)
static basic::Tracer TR ("core.conformation.symmetry.util")
static
numeric::random::RandomGenerator 
RG (408529)
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)
kinematics::FoldTree set_fold_tree_from_symm_data (conformation::Conformation &src_conformation, conformation::symmetry::SymmData &symmdata)
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)

Typedef Documentation


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

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 = "" 
)

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

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

Attempt to detect whether a conformation is symmetric

Referenced by core::optimization::symmetry::SymMinimizerMap::add_torsion(), protocols::topology_broker::FibrilModelingClaimer::allow_claim(), protocols::topology_broker::TopologyBroker::apply(), protocols::fldsgn::potentials::SetSecStructEnergies::apply(), protocols::fldsgn::CircularPermutation::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::electron_density::dockPoseIntoMap(), core::scoring::methods::MetalloPlacementEnergy::finalize_total_energy(), get_asymm_unit_fold_tree(), protocols::cluster::GatherPosesMover::get_distance_measure(), core::optimization::symmetry::SymAtomTreeMinimizer::make_assymetric_movemap(), core::optimization::symmetry::SymAtomTreeMinimizer::make_semisymmetric_movemap(), core::pack::make_symmetric_PackerTask(), protocols::simple_moves::symmetry::SymEnergyCutRotamerTrialsMover::make_symmetric_task(), protocols::features::DatabaseJobInputter::pose_from_job(), core::optimization::symmetry::SymAtomTreeMinimizer::run(), protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential::score(), 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)
template<class CloneType >
void core::conformation::symmetry::map_to_comma_strings ( std::ostream &  out,
std::map< Size, CloneType >  clones,
std::string  tag = "" 
)

Referenced by operator<<().

void core::conformation::symmetry::map_to_comma_strings ( std::ostream &  out,
std::map< Size, SymDof >  clones,
std::string  tag = "" 
)
std::ostream& core::conformation::symmetry::operator<< ( std::ostream &  s,
const SymDof &  dof 
)
std::ostream& core::conformation::symmetry::operator<< ( std::ostream &  s,
const SymmetryInfo &  symminfo 
)
std::istream& core::conformation::symmetry::operator>> ( std::istream &  s,
SymmetryInfo &  symminfo 
)
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 
)
static numeric::random::RandomGenerator core::conformation::symmetry::RG ( 408529  ) [static]
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 
)
conformation::symmetry::SymmetricConformationOP core::conformation::symmetry::setup_symmetric_conformation ( conformation::Conformation &  src_conformation,
conformation::symmetry::SymmData &  symmdata 
)
void core::conformation::symmetry::shift_jump_numbers_in_dofs ( conformation::Conformation &  conformation,
Size  shift 
)
void core::conformation::symmetry::symmetrize_fold_tree ( core::conformation::Conformation const &  conf,
kinematics::FoldTree &  f 
)
static basic::Tracer core::conformation::symmetry::TR ( "core.conformation.symmetry.symmdatafactory"  ) [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.util"  ) [static]
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 = "" 
)

Referenced by operator<<().

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

Referenced by operator<<().

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