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Rosetta
2020.50
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Classes | |
class | CatPiCalculator |
class | ChargeCalculator |
class | ClashCountCalculator |
class | DecomposeAndReweightEnergiesCalculator |
class | EmptyVertexData |
class | EnergiesData |
class | FragQualCalculator |
class | HPatchCalculator |
class | InterGroupNeighborsCalculator |
class | MetricValueGetter |
class | NeighborhoodByDistanceCalculator |
class | NeighborsByDistanceCalculator |
class | NonlocalContactsCalculator |
class | PackstatCalculator |
class | PiPiCalculator |
class | ResidueDecompositionByChainCalculator |
class | ResidueDecompositionCalculator |
class | RotamerBoltzCalculator |
class | RotamerRecovery |
class | SaltBridgeCalculator |
class | SemiExplicitWaterUnsatisfiedPolarsCalculator |
class | SequenceComparison |
class | SHOBuriedUnsatisfiedPolarsCalculator |
class | SurfaceCalculator |
Functions | |
static basic::Tracer | TR ("protocols.toolbox.PoseMetricCalculators.ExplicitWaterUnsatisfiedPolarsCalculator") |
void | append_rsd_by_jump_near_atom (pose::Pose &pose, core::Size seqpos, core::Size atomno, conformation::Residue new_rsd, core::Size new_atomno, Real dist_min, Real dist_max) |
void | dock_waters_to_atom (pose::Pose &pose, ScoreFunctionOP scorefxn, core::Size seqpos, core::Size atomno, conformation::Residue wat_rsd, core::Size new_atomno, Real dist_min, Real dist_max) |
void | find_res_unsat_polars (Pose const pose, core::Size const seqpos, vector1< bool > &atm_is_unsat) |
core::Real | compute_rmsd (core::pose::Pose const &pose1, core::pose::Pose const &pose2, ObjexxFCL::FArray1D< bool > const &subset) |
bool | fast_clash_check (Pose const &pose, vector1< id::AtomID > const check_atids, Real const clash_dist_cut) |
static basic::Tracer | TR ("seqrecovery") |
static basic::Tracer | TR ("protocols.toolbox.pose_metric_calculators.SHOBuriedUnsatisfiedPolarsCalculator") |
void | residue_subset (std::string setf, utility::vector1< core::Size > &rset, core::pose::Pose &ps) |
extracts the pose indexes of a selected subset of residues More... | |
typedef utility::pointer::shared_ptr< DecomposeAndReweightEnergiesCalculator const > protocols::pose_metric_calculators::DecomposeAndReweightEnergiesCalculatorCOP |
typedef utility::pointer::shared_ptr< DecomposeAndReweightEnergiesCalculator > protocols::pose_metric_calculators::DecomposeAndReweightEnergiesCalculatorOP |
typedef std::pair< one_group, one_group > protocols::pose_metric_calculators::group_pair |
using protocols::pose_metric_calculators::group_set = typedef utility::vector1<group_pair> |
typedef utility::pointer::shared_ptr< InterGroupNeighborsCalculator const > protocols::pose_metric_calculators::InterGroupNeighborsCalculatorCOP |
typedef utility::pointer::shared_ptr< InterGroupNeighborsCalculator > protocols::pose_metric_calculators::InterGroupNeighborsCalculatorOP |
typedef utility::pointer::shared_ptr< NeighborhoodByDistanceCalculator const > protocols::pose_metric_calculators::NeighborhoodByDistanceCalculatorCOP |
typedef utility::pointer::shared_ptr< NeighborhoodByDistanceCalculator > protocols::pose_metric_calculators::NeighborhoodByDistanceCalculatorOP |
typedef utility::pointer::shared_ptr< NeighborsByDistanceCalculator const > protocols::pose_metric_calculators::NeighborsByDistanceCalculatorCOP |
typedef utility::pointer::shared_ptr< NeighborsByDistanceCalculator > protocols::pose_metric_calculators::NeighborsByDistanceCalculatorOP |
using protocols::pose_metric_calculators::one_group = typedef std::set<core::Size> |
using protocols::pose_metric_calculators::parent = typedef core::pose::metrics::StructureDependentCalculator |
typedef utility::pointer::shared_ptr< ResidueDecompositionByChainCalculator const > protocols::pose_metric_calculators::ResidueDecompositionByChainCalculatorCOP |
typedef utility::pointer::shared_ptr< ResidueDecompositionByChainCalculator > protocols::pose_metric_calculators::ResidueDecompositionByChainCalculatorOP |
typedef utility::pointer::shared_ptr< RotamerBoltzCalculator const > protocols::pose_metric_calculators::RotamerBoltzCalculatorCOP |
typedef utility::pointer::shared_ptr< RotamerBoltzCalculator> protocols::pose_metric_calculators::RotamerBoltzCalculatorOP |
typedef std::map< core::Size, RotamerProbability > protocols::pose_metric_calculators::RotamerProbabilities |
typedef utility::pointer::shared_ptr< SHOBuriedUnsatisfiedPolarsCalculator const > protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculatorCOP |
typedef utility::pointer::shared_ptr< SHOBuriedUnsatisfiedPolarsCalculator > protocols::pose_metric_calculators::SHOBuriedUnsatisfiedPolarsCalculatorOP |
void protocols::pose_metric_calculators::append_rsd_by_jump_near_atom | ( | pose::Pose & | pose, |
core::Size | seqpos, | ||
core::Size | atomno, | ||
conformation::Residue | new_rsd, | ||
core::Size | new_atomno, | ||
Real | dist_min, | ||
Real | dist_max | ||
) |
References core::pose::Pose::append_residue_by_jump(), core::conformation::Residue::atom_name(), core::pose::Pose::fold_tree(), core::pose::Pose::jump(), core::kinematics::FoldTree::num_jump(), protocols::geometry::random_reorientation_matrix(), core::pose::Pose::residue(), core::scoring::rg, core::pose::Pose::set_jump(), and core::pose::Pose::size().
Referenced by dock_waters_to_atom().
core::Real protocols::pose_metric_calculators::compute_rmsd | ( | core::pose::Pose const & | pose1, |
core::pose::Pose const & | pose2, | ||
ObjexxFCL::FArray1D< bool > const & | subset | ||
) |
void protocols::pose_metric_calculators::dock_waters_to_atom | ( | pose::Pose & | pose, |
ScoreFunctionOP | scorefxn, | ||
core::Size | seqpos, | ||
core::Size | atomno, | ||
conformation::Residue | wat_rsd, | ||
core::Size | new_atomno, | ||
Real | dist_min, | ||
Real | dist_max | ||
) |
bool protocols::pose_metric_calculators::fast_clash_check | ( | Pose const & | pose, |
vector1< id::AtomID > const | check_atids, | ||
Real const | clash_dist_cut | ||
) |
References core::conformation::Residue::atom_type(), core::chemical::AtomType::lj_wdepth(), core::conformation::Residue::natoms(), core::pose::Pose::residue(), core::pose::Pose::size(), and core::pose::Pose::xyz().
Referenced by protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::semiexpl_water_hbgeom_score().
void protocols::pose_metric_calculators::find_res_unsat_polars | ( | Pose const | pose, |
core::Size const | seqpos, | ||
vector1< bool > & | atm_is_unsat | ||
) |
void protocols::pose_metric_calculators::residue_subset | ( | std::string | setf, |
utility::vector1< core::Size > & | rset, | ||
core::pose::Pose & | ps | ||
) |
extracts the pose indexes of a selected subset of residues
[in] | setf | path to a file specifying the residue subset according to the following format: |
C1 R1 I1
... CN RN IN
Here, Ci, Ri, and Ii indicate the chain identifier, residue index, and insertion code (as specified in the pose's input PDB file) of the ith residue in the subset (i=1,...,N; N>=1).
[out] | rset | vector to hold the residue indexes. The vector must be passed empty. |
[in] | ps | the pose. |
: after this function has been called, rset[i] is the pose index of the residue specified by the ith input line (i=1,...,N).
: blank chain identifiers and insertion codes must be specified with the '_' character.
References core::pose::Pose::pdb_info(), and TR().
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Referenced by protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::assert_calculators(), protocols::pose_metric_calculators::RotamerBoltzCalculator::compute_boltz_weight_packrotamers(), protocols::pose_metric_calculators::RotamerBoltzCalculator::computeAllBoltz(), protocols::pose_metric_calculators::SequenceComparison::fill_designable_set(), protocols::pose_metric_calculators::SequenceComparison::get_sequence_recovery(), protocols::pose_metric_calculators::FragQualCalculator::lookup(), protocols::pose_metric_calculators::NeighborsByDistanceCalculator::recompute(), protocols::pose_metric_calculators::NonlocalContactsCalculator::recompute(), protocols::pose_metric_calculators::SemiExplicitWaterUnsatisfiedPolarsCalculator::recompute(), protocols::pose_metric_calculators::FragQualCalculator::recompute(), and residue_subset().