rms_util.tmpl.hh File Reference

#include <core/types.hh>
#include <core/pose/Pose.hh>
#include <core/conformation/Residue.hh>
#include <core/scoring/rms_util.hh>
#include <numeric/model_quality/rms.hh>
#include <numeric/xyzVector.hh>
#include <ObjexxFCL/FArray1D.hh>
#include <ObjexxFCL/FArray2D.hh>
#include <ObjexxFCL/FArray1A.hh>
#include <ObjexxFCL/FArray2A.hh>
#include <list>
#include <platform/types.hh>
#include <core/chemical/AA.hh>
#include <core/chemical/Adduct.fwd.hh>
#include <core/chemical/Adduct.hh>
#include <core/chemical/AtomICoor.fwd.hh>
#include <core/chemical/AtomICoor.hh>
#include <core/chemical/AtomType.fwd.hh>
#include <core/chemical/AtomType.hh>
#include <core/chemical/AtomTypeSet.fwd.hh>
#include <core/chemical/ElementSet.fwd.hh>
#include <core/chemical/MMAtomType.fwd.hh>
#include <core/chemical/MMAtomTypeSet.fwd.hh>
#include <core/chemical/ResConnID.fwd.hh>
#include <core/chemical/ResConnID.hh>
#include <core/chemical/ResidueConnection.fwd.hh>
#include <core/chemical/ResidueConnection.hh>
#include <core/chemical/ResidueType.fwd.hh>
#include <core/chemical/ResidueType.hh>
#include <core/chemical/ResidueTypeSet.fwd.hh>
#include <core/chemical/VariantType.fwd.hh>
#include <core/chemical/types.hh>
#include <core/chemical/orbitals/ICoorOrbitalData.hh>
#include <core/chemical/orbitals/OrbitalType.fwd.hh>
#include <core/chemical/orbitals/OrbitalTypeSet.fwd.hh>
#include <core/chemical/sdf/MolData.fwd.hh>
#include <core/chemical/sdf/MolData.hh>
#include <core/conformation/Atom.fwd.hh>
#include <core/conformation/Atom.hh>
#include <core/conformation/Conformation.fwd.hh>
#include <core/conformation/Conformation.hh>
#include <core/conformation/PseudoBond.fwd.hh>
#include <core/conformation/Residue.fwd.hh>
#include <core/conformation/orbitals/OrbitalXYZCoords.hh>
#include <core/conformation/signals/ConnectionEvent.fwd.hh>
#include <core/conformation/signals/ConnectionEvent.hh>
#include <core/conformation/signals/GeneralEvent.fwd.hh>
#include <core/conformation/signals/GeneralEvent.hh>
#include <core/conformation/signals/IdentityEvent.fwd.hh>
#include <core/conformation/signals/IdentityEvent.hh>
#include <core/conformation/signals/LengthEvent.fwd.hh>
#include <core/conformation/signals/LengthEvent.hh>
#include <core/conformation/signals/XYZEvent.fwd.hh>
#include <core/conformation/signals/XYZEvent.hh>
#include <core/conformation/symmetry/SymDof.fwd.hh>
#include <core/conformation/symmetry/SymSlideInfo.fwd.hh>
#include <core/conformation/symmetry/SymSlideInfo.hh>
#include <core/conformation/symmetry/SymmData.fwd.hh>
#include <core/conformation/symmetry/SymmetricConformation.fwd.hh>
#include <core/conformation/symmetry/SymmetricConformation.hh>
#include <core/conformation/symmetry/SymmetryInfo.fwd.hh>
#include <core/conformation/symmetry/SymmetryInfo.hh>
#include <core/id/AtomID.fwd.hh>
#include <core/id/AtomID.hh>
#include <core/id/AtomID_Map.fwd.hh>
#include <core/id/AtomID_Map.hh>
#include <core/id/AtomID_Mask.fwd.hh>
#include <core/id/DOF_ID.fwd.hh>
#include <core/id/DOF_ID.hh>
#include <core/id/DOF_ID_Map.fwd.hh>
#include <core/id/DOF_ID_Mask.fwd.hh>
#include <core/id/NamedAtomID.fwd.hh>
#include <core/id/NamedAtomID.hh>
#include <core/id/NamedStubID.fwd.hh>
#include <core/id/SequenceMapping.hh>
#include <core/id/TorsionID.fwd.hh>
#include <core/id/types.hh>
#include <core/kinematics/AtomPointer.fwd.hh>
#include <core/kinematics/AtomTree.fwd.hh>
#include <core/kinematics/AtomTree.hh>
#include <core/kinematics/AtomWithDOFChange.fwd.hh>
#include <core/kinematics/DomainMap.fwd.hh>
#include <core/kinematics/Edge.fwd.hh>
#include <core/kinematics/Edge.hh>
#include <core/kinematics/FoldTree.fwd.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/kinematics/Jump.fwd.hh>
#include <core/kinematics/Jump.hh>
#include <core/kinematics/MinimizerMapBase.fwd.hh>
#include <core/kinematics/RT.fwd.hh>
#include <core/kinematics/RT.hh>
#include <core/kinematics/ResidueCoordinateChangeList.fwd.hh>
#include <core/kinematics/Stub.fwd.hh>
#include <core/kinematics/Stub.hh>
#include <core/kinematics/tree/Atom.fwd.hh>
#include <core/kinematics/tree/Atom.hh>
#include <core/pose/PDBInfo.fwd.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/pose/datacache/ObserverCache.fwd.hh>
#include <core/pose/metrics/PoseMetricContainer.fwd.hh>
#include <core/pose/signals/ConformationEvent.fwd.hh>
#include <core/pose/signals/DestructionEvent.fwd.hh>
#include <core/pose/signals/EnergyEvent.fwd.hh>
#include <core/pose/signals/GeneralEvent.fwd.hh>
#include <core/scoring/Energies.fwd.hh>
#include <core/scoring/ScoreFunction.fwd.hh>
#include <core/scoring/constraints/Constraint.fwd.hh>
#include <core/scoring/constraints/ConstraintSet.fwd.hh>
#include <utility/Bound.fwd.hh>
#include <utility/Bound.hh>
#include <utility/assert.hh>
#include <utility/down_cast.hh>
#include <utility/exit.hh>
#include <utility/stream_util.hh>
#include <utility/string_util.hh>
#include <utility/vector0_bool.hh>
#include <utility/vector1.fwd.hh>
#include <utility/vector1.hh>
#include <utility/vector1_bool.hh>
#include <utility/vectorL.fwd.hh>
#include <utility/vectorL.hh>
#include <utility/vectorL_Selector.hh>
#include <utility/vectorL_bool.hh>
#include <utility/file/FileName.fwd.hh>
#include <utility/file/FileName.hh>
#include <utility/file/PathName.fwd.hh>
#include <utility/file/PathName.hh>
#include <utility/keys/AutoKey.fwd.hh>
#include <utility/keys/AutoKey.hh>
#include <utility/keys/Key.fwd.hh>
#include <utility/keys/Key.hh>
#include <utility/keys/Key2Tuple.fwd.hh>
#include <utility/keys/Key2Tuple.hh>
#include <utility/keys/Key3Tuple.fwd.hh>
#include <utility/keys/Key3Tuple.hh>
#include <utility/keys/Key4Tuple.fwd.hh>
#include <utility/keys/Key4Tuple.hh>
#include <utility/keys/KeyLess.fwd.hh>
#include <utility/keys/KeyLookup.fwd.hh>
#include <utility/keys/KeyLookup.hh>
#include <utility/keys/NoClient.fwd.hh>
#include <utility/keys/NoClient.hh>
#include <utility/keys/SmallKeyVector.fwd.hh>
#include <utility/keys/SmallKeyVector.hh>
#include <utility/keys/UserKey.fwd.hh>
#include <utility/keys/VariantKey.fwd.hh>
#include <utility/keys/VariantKey.hh>
#include <utility/options/AnyOption.fwd.hh>
#include <utility/options/AnyOption.hh>
#include <utility/options/AnyVectorOption.fwd.hh>
#include <utility/options/AnyVectorOption.hh>
#include <utility/options/BooleanOption.fwd.hh>
#include <utility/options/BooleanOption.hh>
#include <utility/options/BooleanVectorOption.fwd.hh>
#include <utility/options/BooleanVectorOption.hh>
#include <utility/options/FileOption.fwd.hh>
#include <utility/options/FileOption.hh>
#include <utility/options/FileVectorOption.fwd.hh>
#include <utility/options/FileVectorOption.hh>
#include <utility/options/IntegerOption.fwd.hh>
#include <utility/options/IntegerOption.hh>
#include <utility/options/IntegerVectorOption.fwd.hh>
#include <utility/options/IntegerVectorOption.hh>
#include <utility/options/Option.fwd.hh>
#include <utility/options/Option.hh>
#include <utility/options/OptionCollection.fwd.hh>
#include <utility/options/OptionCollection.hh>
#include <utility/options/PathOption.fwd.hh>
#include <utility/options/PathOption.hh>
#include <utility/options/PathVectorOption.fwd.hh>
#include <utility/options/PathVectorOption.hh>
#include <utility/options/RealOption.fwd.hh>
#include <utility/options/RealOption.hh>
#include <utility/options/RealVectorOption.fwd.hh>
#include <utility/options/RealVectorOption.hh>
#include <utility/options/ScalarOption.fwd.hh>
#include <utility/options/ScalarOption.hh>
#include <utility/options/ScalarOption_T_.fwd.hh>
#include <utility/options/ScalarOption_T_.hh>
#include <utility/options/StringOption.fwd.hh>
#include <utility/options/StringOption.hh>
#include <utility/options/StringVectorOption.fwd.hh>
#include <utility/options/StringVectorOption.hh>
#include <utility/options/VariantOption.fwd.hh>
#include <utility/options/VariantOption.hh>
#include <utility/options/VectorOption.fwd.hh>
#include <utility/options/VectorOption.hh>
#include <utility/options/VectorOption_T_.fwd.hh>
#include <utility/options/VectorOption_T_.hh>
#include <utility/options/mpi_stderr.hh>
#include <utility/options/keys/AnyOptionKey.fwd.hh>
#include <utility/options/keys/AnyOptionKey.hh>
#include <utility/options/keys/AnyVectorOptionKey.fwd.hh>
#include <utility/options/keys/AnyVectorOptionKey.hh>
#include <utility/options/keys/BooleanOptionKey.fwd.hh>
#include <utility/options/keys/BooleanOptionKey.hh>
#include <utility/options/keys/BooleanVectorOptionKey.fwd.hh>
#include <utility/options/keys/BooleanVectorOptionKey.hh>
#include <utility/options/keys/FileOptionKey.fwd.hh>
#include <utility/options/keys/FileOptionKey.hh>
#include <utility/options/keys/FileVectorOptionKey.fwd.hh>
#include <utility/options/keys/FileVectorOptionKey.hh>
#include <utility/options/keys/IntegerOptionKey.fwd.hh>
#include <utility/options/keys/IntegerOptionKey.hh>
#include <utility/options/keys/IntegerVectorOptionKey.fwd.hh>
#include <utility/options/keys/IntegerVectorOptionKey.hh>
#include <utility/options/keys/OptionKey.fwd.hh>
#include <utility/options/keys/OptionKey.hh>
#include <utility/options/keys/OptionKeys.hh>
#include <utility/options/keys/PathOptionKey.fwd.hh>
#include <utility/options/keys/PathOptionKey.hh>
#include <utility/options/keys/PathVectorOptionKey.fwd.hh>
#include <utility/options/keys/PathVectorOptionKey.hh>
#include <utility/options/keys/RealOptionKey.fwd.hh>
#include <utility/options/keys/RealOptionKey.hh>
#include <utility/options/keys/RealVectorOptionKey.fwd.hh>
#include <utility/options/keys/RealVectorOptionKey.hh>
#include <utility/options/keys/ScalarOptionKey.fwd.hh>
#include <utility/options/keys/ScalarOptionKey.hh>
#include <utility/options/keys/StringOptionKey.fwd.hh>
#include <utility/options/keys/StringOptionKey.hh>
#include <utility/options/keys/StringVectorOptionKey.fwd.hh>
#include <utility/options/keys/StringVectorOptionKey.hh>
#include <utility/options/keys/VectorOptionKey.fwd.hh>
#include <utility/options/keys/VectorOptionKey.hh>
#include <utility/options/keys/all.hh>
#include <utility/pointer/ReferenceCount.fwd.hh>
#include <utility/pointer/ReferenceCount.hh>
#include <utility/pointer/access_ptr.fwd.hh>
#include <utility/pointer/access_ptr.hh>
#include <utility/pointer/owning_ptr.functions.hh>
#include <utility/pointer/owning_ptr.fwd.hh>
#include <utility/pointer/owning_ptr.hh>
#include <utility/signals/BufferedSignalHub.fwd.hh>
#include <utility/signals/BufferedSignalHub.hh>
#include <utility/signals/Link.fwd.hh>
#include <utility/signals/Link.hh>
#include <utility/signals/LinkUnit.fwd.hh>
#include <utility/signals/LinkUnit.hh>
#include <utility/signals/PausableSignalHub.fwd.hh>
#include <utility/signals/PausableSignalHub.hh>
#include <utility/signals/SignalHub.fwd.hh>
#include <utility/signals/SignalHub.hh>
#include <numeric/HomogeneousTransform.hh>
#include <numeric/NumericTraits.hh>
#include <numeric/constants.hh>
#include <numeric/conversions.hh>
#include <numeric/numeric.functions.hh>
#include <numeric/sphericalVector.fwd.hh>
#include <numeric/sphericalVector.hh>
#include <numeric/trig.functions.hh>
#include <numeric/types.hh>
#include <numeric/xyz.functions.fwd.hh>
#include <numeric/xyz.functions.hh>
#include <numeric/xyzMatrix.fwd.hh>
#include <numeric/xyzMatrix.hh>
#include <numeric/xyzVector.fwd.hh>
#include <numeric/internal/ColPointers.hh>
#include <numeric/internal/ColVectors.hh>
#include <numeric/internal/ColsPointer.hh>
#include <numeric/internal/RowPointers.hh>
#include <numeric/internal/RowVectors.hh>
#include <numeric/internal/RowsPointer.hh>
#include <ObjexxFCL/Dimension.fwd.hh>
#include <ObjexxFCL/Dimension.hh>
#include <ObjexxFCL/DimensionExpression.hh>
#include <ObjexxFCL/DynamicIndexRange.fwd.hh>
#include <ObjexxFCL/DynamicIndexRange.hh>
#include <ObjexxFCL/FArray.all.fwd.hh>
#include <ObjexxFCL/FArray.fwd.hh>
#include <ObjexxFCL/FArray.hh>
#include <ObjexxFCL/FArray1.all.fwd.hh>
#include <ObjexxFCL/FArray1.fwd.hh>
#include <ObjexxFCL/FArray1.hh>
#include <ObjexxFCL/FArray1A.fwd.hh>
#include <ObjexxFCL/FArray1D.fwd.hh>
#include <ObjexxFCL/FArray1P.fwd.hh>
#include <ObjexxFCL/FArray1P.hh>
#include <ObjexxFCL/FArray2.all.fwd.hh>
#include <ObjexxFCL/FArray2.fwd.hh>
#include <ObjexxFCL/FArray2.hh>
#include <ObjexxFCL/FArray2A.fwd.hh>
#include <ObjexxFCL/FArray2D.fwd.hh>
#include <ObjexxFCL/FArray2P.fwd.hh>
#include <ObjexxFCL/FArray2P.hh>
#include <ObjexxFCL/FArray3.all.fwd.hh>
#include <ObjexxFCL/FArray3.fwd.hh>
#include <ObjexxFCL/FArray3A.fwd.hh>
#include <ObjexxFCL/FArray3D.fwd.hh>
#include <ObjexxFCL/FArray3P.fwd.hh>
#include <ObjexxFCL/FArray4.all.fwd.hh>
#include <ObjexxFCL/FArray4.fwd.hh>
#include <ObjexxFCL/FArray4A.fwd.hh>
#include <ObjexxFCL/FArray4D.fwd.hh>
#include <ObjexxFCL/FArray4P.fwd.hh>
#include <ObjexxFCL/FArray5.all.fwd.hh>
#include <ObjexxFCL/FArray5.fwd.hh>
#include <ObjexxFCL/FArray5A.fwd.hh>
#include <ObjexxFCL/FArray5D.fwd.hh>
#include <ObjexxFCL/FArray5P.fwd.hh>
#include <ObjexxFCL/FArray6.all.fwd.hh>
#include <ObjexxFCL/FArray6.fwd.hh>
#include <ObjexxFCL/FArray6A.fwd.hh>
#include <ObjexxFCL/FArray6D.fwd.hh>
#include <ObjexxFCL/FArray6P.fwd.hh>
#include <ObjexxFCL/FArrayInitializer.fwd.hh>
#include <ObjexxFCL/FArrayInitializer.hh>
#include <ObjexxFCL/FArraySection.fwd.hh>
#include <ObjexxFCL/FArraySection.hh>
#include <ObjexxFCL/FArrayTraits.fwd.hh>
#include <ObjexxFCL/FArrayTraits.hh>
#include <ObjexxFCL/IndexRange.fwd.hh>
#include <ObjexxFCL/IndexRange.hh>
#include <ObjexxFCL/InitializerSentinel.hh>
#include <ObjexxFCL/KeyFArray1D.fwd.hh>
#include <ObjexxFCL/KeyFArray2D.fwd.hh>
#include <ObjexxFCL/KeyFArray3D.fwd.hh>
#include <ObjexxFCL/KeyFArray4D.fwd.hh>
#include <ObjexxFCL/KeyFArray5D.fwd.hh>
#include <ObjexxFCL/KeyFArray6D.fwd.hh>
#include <ObjexxFCL/Observer.fwd.hh>
#include <ObjexxFCL/Observer.hh>
#include <ObjexxFCL/ObserverMulti.hh>
#include <ObjexxFCL/ObserverSingle.hh>
#include <ObjexxFCL/ProxySentinel.hh>
#include <ObjexxFCL/SetWrapper.fwd.hh>
#include <ObjexxFCL/Star.fwd.hh>
#include <ObjexxFCL/Star.hh>
#include <ObjexxFCL/StaticIndexRange.fwd.hh>
#include <ObjexxFCL/StaticIndexRange.hh>
#include <ObjexxFCL/TypeTraits.hh>
#include <ObjexxFCL/char.functions.hh>
#include <ObjexxFCL/proxy_const_assert.hh>
#include <ObjexxFCL/string.functions.hh>
#include <algorithm>
#include <cassert>
#include <cmath>
#include <cstddef>
#include <cstdio>
#include <cstdlib>
#include <iomanip>
#include <iosfwd>
#include <iostream>
#include <limits>
#include <map>
#include <ostream>
#include <set>
#include <sstream>
#include <string>
#include <typeinfo>
#include <utility>
#include <vector>
#include <basic/MetricValue.fwd.hh>
#include <basic/datacache/BasicDataCache.fwd.hh>
#include <basic/options/keys/OptionKeys.hh>
#include <basic/options/option.hh>
#include <boost/algorithm/string/erase.hpp>
#include <boost/bind.hpp>
#include <boost/foreach.hpp>
#include <boost/function.hpp>
#include <boost/functional/hash.hpp>
#include <boost/unordered/unordered_map.hpp>

Namespaces
	core
	A class for defining atom parameters, known as atom_types.
	core::scoring

Functions
template<class T >
core::Real	core::scoring::rmsd_with_super (core::pose::Pose const &pose1, core::pose::Pose const &pose2, std::list< core::Size > const &subset_residues, T *predicate)
template<class T >
core::Real	core::scoring::rmsd_with_super (core::pose::Pose const &pose1, core::pose::Pose const &pose2, T *predicate)
	Select atoms for RMS via a predicate function/functor. More...
template<class T >
core::Real	core::scoring::rmsd_with_super_subset (core::pose::Pose const &pose1, core::pose::Pose const &pose2, ObjexxFCL::FArray1D_bool const &subset, T *predicate)
	Select a subset atoms for RMS via a predicate function/functor. More...
template<class T >
core::Real	core::scoring::rmsd_no_super (core::pose::Pose const &pose1, core::pose::Pose const &pose2, T *predicate)
	Select atoms for RMS via a predicate function/functor. More...
template<class T >
core::Real	core::scoring::rmsd_no_super (core::conformation::ResidueCOPs const &residues1, core::conformation::ResidueCOPs const &residues2, T *predicate)
template<class T >
core::Real	core::scoring::rmsd_no_super_subset (core::pose::Pose const &pose1, core::pose::Pose const &pose2, ObjexxFCL::FArray1D_bool const &subset, T *predicate)
	Select atoms for RMS via a predicate function/functor. More...
template<class T >
core::Real	core::scoring::rmsd_no_super_subset (core::pose::Pose const &pose1, core::pose::Pose const &pose2, ObjexxFCL::FArray1D_bool const &subset, core::id::SequenceMapping const &seqmap, T *predicate)
	like function above, but uses sequence mapping, i.e. sections of poses of different lengths can be compared at the moment sorta assumes that residues at corresponding positions have the same identity, mainly becaue the predicates are structured that way... More...
template<class T >
core::Real	core::scoring::biggest_residue_deviation_no_super (core::pose::Pose const &pose1, core::pose::Pose const &pose2, T *predicate)
	function to return the biggest deviation between an atom in a pair of poses, More...
template<class T >
core::Real	core::scoring::biggest_residue_deviation_no_super_subset (core::pose::Pose const &pose1, core::pose::Pose const &pose2, ObjexxFCL::FArray1D_bool const &subset, T *predicate)
	function to return the biggest deviation between an atom in a pair of poses, More...
template<class T >
void	core::scoring::fill_rmsd_coordinates (int &natoms, ObjexxFCL::FArray2D< core::Real > &p1a, ObjexxFCL::FArray2D< core::Real > &p2a, core::pose::Pose const &pose1, core::pose::Pose const &pose2, T *predicate)
template<class T >
core::Real	core::scoring::sym_rmsd_with_super_subset (core::pose::Pose const &native_pose, core::pose::Pose const &pose2, ObjexxFCL::FArray1D_bool const &subset, T *predicate)
	Select a subset atoms for Symmetric RMS via a predicate function/functor. Example of use, to calculate C-alpha RMSD: rmsd_with_super(pose1, pose2, is_protein_CA, subset);. More...