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Rosetta
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#include <core/types.hh>#include <core/conformation/Residue.hh>#include <core/chemical/ResidueTypeSet.hh>#include <core/chemical/ChemicalManager.hh>#include <core/pose/Pose.hh>#include <basic/options/option.hh>#include <basic/options/after_opts.hh>#include <basic/Tracer.hh>#include <devel/init.hh>#include <core/io/pdb/pdb_writer.hh>#include <core/import_pose/pose_stream/util.hh>#include <core/import_pose/pose_stream/MetaPoseInputStream.hh>#include <core/sequence/util.hh>#include <core/sequence/Sequence.hh>#include <core/sequence/Sequence.fwd.hh>#include <core/id/SequenceMapping.hh>#include <core/sequence/SequenceAlignment.hh>#include <core/sequence/ScoringScheme.fwd.hh>#include <core/sequence/SimpleScoringScheme.hh>#include <core/sequence/SWAligner.hh>#include <utility/vector1.hh>#include <ObjexxFCL/string.functions.hh>#include <numeric/model_quality/rms.hh>#include <apps/pilot/james/james_util.hh>#include <string>#include <basic/options/keys/in.OptionKeys.gen.hh>#include <basic/options/keys/out.OptionKeys.gen.hh>#include <basic/options/keys/james.OptionKeys.gen.hh>#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/AtomTypeSet.hh>#include <core/chemical/ChemicalManager.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/ResidueTypeSelector.fwd.hh>#include <core/chemical/ResidueType.fwd.hh>#include <core/chemical/ResidueType.hh>#include <core/chemical/ResidueTypeSet.fwd.hh>#include <core/chemical/VariantType.hh>#include <core/chemical/types.hh>#include <core/conformation/Atom.fwd.hh>#include <core/conformation/Atom.hh>#include <core/conformation/Conformation.fwd.hh>#include <core/conformation/PseudoBond.fwd.hh>#include <core/conformation/Residue.fwd.hh>#include <core/conformation/signals/LengthEvent.fwd.hh>#include <core/conformation/signals/XYZEvent.fwd.hh>#include <core/id/AtomID.fwd.hh>#include <core/id/AtomID.hh>#include <core/id/AtomID_Map.fwd.hh>#include <core/id/AtomID_Mask.fwd.hh>#include <core/id/DOF_ID.fwd.hh>#include <core/id/DOF_ID.hh>#include <core/id/NamedAtomID.fwd.hh>#include <core/id/NamedAtomID.hh>#include <core/id/NamedStubID.fwd.hh>#include <core/id/NamedStubID.hh>#include <core/id/TorsionID.fwd.hh>#include <core/id/types.hh>#include <core/import_pose/import_pose.hh>#include <core/import_pose/pose_stream/PoseInputStream.fwd.hh>#include <core/import_pose/pose_stream/PoseInputStream.hh>#include <core/kinematics/AtomTree.fwd.hh>#include <core/kinematics/FoldTree.fwd.hh>#include <core/kinematics/Jump.fwd.hh>#include <core/kinematics/Stub.fwd.hh>#include <core/pack/dunbrack/RotamerLibrary.fwd.hh>#include <basic/options/keys/OptionKeys.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/ConformationEvent.hh>#include <core/pose/signals/DestructionEvent.fwd.hh>#include <core/pose/signals/DestructionEvent.hh>#include <core/pose/signals/EnergyEvent.fwd.hh>#include <core/pose/signals/EnergyEvent.hh>#include <core/pose/signals/GeneralEvent.fwd.hh>#include <core/pose/signals/GeneralEvent.hh>#include <core/scoring/Energies.fwd.hh>#include <core/scoring/ScoreFunction.fwd.hh>#include <core/scoring/ScoreFunctionInfo.fwd.hh>#include <core/scoring/constraints/Constraint.fwd.hh>#include <core/scoring/constraints/ConstraintSet.fwd.hh>#include <core/scoring/constraints/Constraints.fwd.hh>#include <core/sequence/ScoringScheme.hh>#include <core/sequence/SequenceAlignment.fwd.hh>#include <core/id/SequenceMapping.fwd.hh>#include <basic/MetricValue.fwd.hh>#include <utility/stream_util.hh>#include <basic/Tracer.fwd.hh>#include <basic/datacache/BasicDataCache.fwd.hh>#include <utility/Bound.fwd.hh>#include <utility/Bound.hh>#include <utility/down_cast.hh>#include <utility/exit.hh>#include <utility/vector1.fwd.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/io/izstream.fwd.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/VirtualBase.fwd.hh>#include <utility/VirtualBase.hh>#include <utility/pointer/access_ptr.hh>#include <utility/pointer/owning_ptr.functions.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/SignalHub.fwd.hh>#include <utility/signals/SignalHub.hh>#include <numeric/numeric.functions.hh>#include <numeric/trig.functions.hh>#include <numeric/types.hh>#include <numeric/xyz.functions.fwd.hh>#include <numeric/xyzMatrix.fwd.hh>#include <numeric/xyzVector.fwd.hh>#include <numeric/xyzVector.hh>#include <numeric/model_quality/RmsData.hh>#include <numeric/random/random.fwd.hh>#include <numeric/random/random.hh>#include <numeric/random/uniform.hh>#include <ObjexxFCL/CArray.fwd.hh>#include <ObjexxFCL/ChunkVector.fwd.hh>#include <ObjexxFCL/Cstring.fwd.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.hh>#include <ObjexxFCL/FArray1.fwd.hh>#include <ObjexxFCL/FArray1.hh>#include <ObjexxFCL/FArray1A.fwd.hh>#include <ObjexxFCL/FArray1A.hh>#include <ObjexxFCL/FArray1D.fwd.hh>#include <ObjexxFCL/FArray1D.hh>#include <ObjexxFCL/FArray1P.fwd.hh>#include <ObjexxFCL/FArray1P.hh>#include <ObjexxFCL/FArray2.fwd.hh>#include <ObjexxFCL/FArray2.hh>#include <ObjexxFCL/FArray2A.fwd.hh>#include <ObjexxFCL/FArray2A.hh>#include <ObjexxFCL/FArray2D.fwd.hh>#include <ObjexxFCL/FArray2D.hh>#include <ObjexxFCL/FArray2P.fwd.hh>#include <ObjexxFCL/FArray2P.hh>#include <ObjexxFCL/FArray3.fwd.hh>#include <ObjexxFCL/FArray3A.fwd.hh>#include <ObjexxFCL/FArray3D.fwd.hh>#include <ObjexxFCL/FArray3P.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.fwd.hh>#include <ObjexxFCL/FArray5A.fwd.hh>#include <ObjexxFCL/FArray5D.fwd.hh>#include <ObjexxFCL/FArray5P.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/Fstring.fwd.hh>#include <ObjexxFCL/IndexRange.fwd.hh>#include <ObjexxFCL/IndexRange.hh>#include <ObjexxFCL/KeyFArray1D.fwd.hh>#include <ObjexxFCL/KeyFArray2D.fwd.hh>#include <ObjexxFCL/KeyFArray3D.fwd.hh>#include <ObjexxFCL/Observer.fwd.hh>#include <ObjexxFCL/Observer.hh>#include <ObjexxFCL/ObserverMulti.hh>#include <ObjexxFCL/ObserverSingle.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/sbyte.fwd.hh>#include <ObjexxFCL/ubyte.fwd.hh>#include <algorithm>#include <cassert>#include <cmath>#include <cstddef>#include <cstdlib>#include <iomanip>#include <iosfwd>#include <iostream>#include <limits>#include <list>#include <map>#include <ostream>#include <set>#include <sstream>#include <utility>#include <vector>#include <utility/excn/Exceptions.hh>Classes | |
| class | SequenceCoords |
| class | RMS_ScoringScheme |
Typedefs | |
| typedef utility::pointer::shared_ptr< SequenceCoords > | SequenceCoordsOP |
Functions | |
| utility::vector1< core::PointPosition > | forward_in_time (FArray2D< numeric::Real > p1, int const natoms) |
| FArray2D< core::Real > | back_in_time_2d (utility::vector1< core::PointPosition > p1) |
| FArray1D< core::Real > | back_in_time_1d (utility::vector1< numeric::Real > w) |
| core::id::SequenceMapping | extend_mapping_by_threshold (utility::vector1< core::PointPosition > &, utility::vector1< core::PointPosition > &, core::id::SequenceMapping const &map) |
| void | apply_rotation (utility::vector1< core::PointPosition > &p2, FArray2D< numeric::Real > uu) |
| FArray2D< numeric::Real > | optimal_rotation (utility::vector1< core::PointPosition > &p1, utility::vector1< core::PointPosition > &p2) |
| Superimposes p2 onto p1, using the SequenceMapping in map. More... | |
| core::id::SequenceMapping | maxsub_align (utility::vector1< core::PointPosition > &p1, utility::vector1< core::PointPosition > &p2, core::id::SequenceMapping const &map) |
| Aligns the points in p1 with the points in p2. The alignment in the provided SequenceMapping is used as to seed the algorithm, and the locally optimal alignment between p1 and p2 is returned. More... | |
| int | main (int argc, char *argv[]) |
| typedef utility::pointer::shared_ptr< SequenceCoords > SequenceCoordsOP |
| void apply_rotation | ( | utility::vector1< core::PointPosition > & | p2, |
| FArray2D< numeric::Real > | uu | ||
| ) |
References create_a3b_hbs::ii, p2, x, predPRE::y, and predPRE::z.
Referenced by maxsub_align().
| FArray1D< core::Real > back_in_time_1d | ( | utility::vector1< numeric::Real > | w | ) |
References create_a3b_hbs::ii, natoms(), and w.
| FArray2D< core::Real > back_in_time_2d | ( | utility::vector1< core::PointPosition > | p1 | ) |
References create_a3b_hbs::ii, and kk.
Referenced by optimal_rotation().
| core::id::SequenceMapping extend_mapping_by_threshold | ( | utility::vector1< core::PointPosition > & | , |
| utility::vector1< core::PointPosition > & | , | ||
| core::id::SequenceMapping const & | map | ||
| ) |
References create_a3b_hbs::ii.
Referenced by maxsub_align().
| utility::vector1< core::PointPosition > forward_in_time | ( | FArray2D< numeric::Real > | p1, |
| int const | natoms | ||
| ) |
References create_a3b_hbs::ii, natoms(), and erraser_analysis::temp.
| int main | ( | int | argc, |
| char * | argv[] | ||
| ) |
References argv, basic::options::OptionKeys::chemical::chemical, utility::io::oc::cout, test.T009_Exceptions::e, basic::init(), in::file::native(), docking::native_pose, option, pyrosetta.distributed.io::pose_from_file, RMS_ScoringScheme::RMS_ScoringScheme(), basic::options::OptionKeys::relax::sequence, challenge::ss, and in::file::template_pdb().
| core::id::SequenceMapping maxsub_align | ( | utility::vector1< core::PointPosition > & | p1, |
| utility::vector1< core::PointPosition > & | p2, | ||
| core::id::SequenceMapping const & | map | ||
| ) |
Aligns the points in p1 with the points in p2. The alignment in the provided SequenceMapping is used as to seed the algorithm, and the locally optimal alignment between p1 and p2 is returned.
References apply_rotation(), extend_mapping_by_threshold(), create_a3b_hbs::ii, beta_nonlocal::jj, optimal_rotation(), and p2.
| FArray2D< numeric::Real > optimal_rotation | ( | utility::vector1< core::PointPosition > & | p1, |
| utility::vector1< core::PointPosition > & | p2 | ||
| ) |
Superimposes p2 onto p1, using the SequenceMapping in map.
References back_in_time_2d(), numeric::model_quality::findUU(), natoms(), and p2.
Referenced by maxsub_align().
1.9.1