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Rosetta
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#include <core/types.hh>#include <core/chemical/ResidueTypeSet.hh>#include <core/chemical/ChemicalManager.hh>#include <devel/init.hh>#include <core/pose/Pose.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/scoring/constraints/util.hh>#include <core/scoring/constraints/ConstraintIO.hh>#include <utility/vector1.hh>#include <numeric/xyzVector.hh>#include <ObjexxFCL/format.hh>#include <ObjexxFCL/string.functions.hh>#include <apps/pilot/james/james_util.hh>#include <iostream>#include <string>#include <basic/options/option.hh>#include <basic/options/keys/in.OptionKeys.gen.hh>#include <basic/options/keys/out.OptionKeys.gen.hh>#include <basic/options/keys/constraints.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/AtomTypeSet.fwd.hh>#include <core/chemical/ChemicalManager.fwd.hh>#include <core/chemical/MMAtomType.fwd.hh>#include <core/chemical/MMAtomTypeSet.fwd.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.fwd.hh>#include <core/chemical/VariantType.hh>#include <core/conformation/Conformation.fwd.hh>#include <core/conformation/Residue.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/ConstraintFactory.hh>#include <core/scoring/constraints/ConstraintForest.fwd.hh>#include <core/scoring/constraints/ConstraintSet.fwd.hh>#include <core/scoring/constraints/Constraints.fwd.hh>#include <core/scoring/func/Func.fwd.hh>#include <core/scoring/func/FuncFactory.fwd.hh>#include <core/scoring/func/FuncFactory.hh>#include <basic/MetricValue.fwd.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/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/xyz.functions.fwd.hh>#include <numeric/xyzMatrix.fwd.hh>#include <numeric/xyzVector.fwd.hh>#include <numeric/random/random.fwd.hh>#include <numeric/random/random.hh>#include <numeric/random/uniform.hh>#include <ObjexxFCL/TypeTraits.hh>#include <ObjexxFCL/char.functions.hh>#include <algorithm>#include <cassert>#include <cmath>#include <complex>#include <cstddef>#include <cstdlib>#include <iomanip>#include <iosfwd>#include <limits>#include <list>#include <map>#include <ostream>#include <set>#include <sstream>#include <utility>#include <vector>#include <utility/excn/Exceptions.hh>Functions | |
| int | main (int argc, char *argv[]) |
| int main | ( | int | argc, |
| char * | argv[] | ||
| ) |
References ObjexxFCL::format::A(), ObjexxFCL::abs(), argv, basic::options::OptionKeys::constraints::constraints, basic::options::OptionKeys::james::dist_thresholds, james::dist_thresholds(), DistanceMatrix::distance(), test.T009_Exceptions::e, ObjexxFCL::format::F(), ObjexxFCL::format::I(), create_a3b_hbs::ii, basic::init(), gaussian-sampling::input, beta_nonlocal::jj, kk, basic::options::OptionKeys::james::min_seqsep, TorsionList::n_torsions(), in::file::native(), docking::native_pose, create_a3b_hbs::nres, option, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, in::file::residue_type_set(), runtime_assert, out::file::silent(), ObjexxFCL::string_of(), TorsionList::torsion(), basic::options::OptionKeys::james::torsion_thresholds, james::torsion_thresholds(), tt, basic::options::OptionKeys::inout::dbms::user, and utility_exit_with_message.
1.9.1