|
Rosetta
|
#include <core/chemical/ChemicalManager.hh>#include <core/chemical/ResidueTypeSet.hh>#include <core/chemical/VariantType.hh>#include <core/chemical/util.hh>#include <core/conformation/Residue.hh>#include <core/conformation/ResidueFactory.hh>#include <core/conformation/symmetry/SymmetryInfo.hh>#include <core/conformation/symmetry/SymmetricConformation.hh>#include <core/conformation/symmetry/VirtualCoordinate.hh>#include <core/conformation/symmetry/SymmData.hh>#include <core/conformation/symmetry/SymDof.hh>#include <core/conformation/symmetry/util.hh>#include <core/fragment/ConstantLengthFragSet.hh>#include <core/fragment/FragData.hh>#include <core/fragment/FragmentIO.hh>#include <core/fragment/BBTorsionSRFD.hh>#include <core/fragment/FragSet.hh>#include <core/import_pose/import_pose.hh>#include <devel/init.hh>#include <basic/database/open.hh>#include <core/io/pdb/pdb_writer.hh>#include <core/kinematics/FoldTree.hh>#include <core/kinematics/MoveMap.hh>#include <basic/options/keys/in.OptionKeys.gen.hh>#include <basic/options/keys/out.OptionKeys.gen.hh>#include <basic/options/keys/smhybrid.OptionKeys.gen.hh>#include <basic/options/keys/parser.OptionKeys.gen.hh>#include <basic/options/keys/edensity.OptionKeys.gen.hh>#include <basic/options/option.hh>#include <basic/options/util.hh>#include <core/pack/task/PackerTask.hh>#include <core/pack/task/TaskFactory.hh>#include <core/pack/optimizeH.hh>#include <core/pose/Pose.hh>#include <core/pose/util.hh>#include <core/scoring/constraints/AmbiguousConstraint.hh>#include <core/scoring/constraints/AngleConstraint.hh>#include <core/scoring/constraints/ResDepAngleConstraint.hh>#include <core/scoring/constraints/AtomPairConstraint.hh>#include <core/scoring/constraints/ResDepAtomPairConstraint.hh>#include <core/scoring/constraints/ResDepDihedralConstraint.hh>#include <core/scoring/constraints/ConstraintSet.hh>#include <core/scoring/constraints/DihedralConstraint.hh>#include <core/scoring/func/HarmonicFunc.hh>#include <core/scoring/constraints/MultiConstraint.hh>#include <core/scoring/constraints/util.hh>#include <core/pack/dunbrack/DunbrackRotamer.fwd.hh>#include <core/pack/dunbrack/RotamerLibrary.hh>#include <core/pack/dunbrack/RotamerLibraryScratchSpace.hh>#include <core/scoring/dssp/Dssp.hh>#include <core/scoring/Energies.hh>#include <core/scoring/electron_density/util.hh>#include <core/scoring/packstat/compute_sasa.hh>#include <core/scoring/rms_util.hh>#include <core/scoring/sasa.hh>#include <core/scoring/ScoreFunction.hh>#include <core/scoring/ScoreFunctionFactory.hh>#include <core/scoring/ScoringManager.hh>#include <core/scoring/symmetry/SymmetricScoreFunction.hh>#include <basic/Tracer.hh>#include <numeric/model_quality/rms.hh>#include <numeric/random/random.hh>#include <numeric/xyz.functions.hh>#include <numeric/xyz.io.hh>#include <ObjexxFCL/FArray2D.hh>#include <ObjexxFCL/format.hh>#include <ObjexxFCL/string.functions.hh>#include <protocols/simple_moves/FragmentMover.hh>#include <protocols/electron_density/util.hh>#include <protocols/flxbb/DesignLayerOperation.fwd.hh>#include <protocols/flxbb/DesignLayerOperation.hh>#include <protocols/flxbb/FlxbbDesign.hh>#include <protocols/jobdist/standard_mains.hh>#include <protocols/viewer/viewers.hh>#include <protocols/moves/Mover.hh>#include <protocols/moves/MonteCarlo.hh>#include <protocols/moves/TrialMover.hh>#include <protocols/moves/MoverContainer.hh>#include <protocols/moves/RepeatMover.hh>#include <protocols/minimization_packing/symmetry/SymMinMover.hh>#include <protocols/minimization_packing/symmetry/SymPackRotamersMover.hh>#include <protocols/symmetry/SymDockingInitialPerturbation.hh>#include <protocols/symmetric_docking/SymDockingLowRes.hh>#include <protocols/relax/SimpleMultiRelax.hh>#include <sstream>#include <utility/io/izstream.hh>#include <utility/io/ozstream.hh>#include <apps/pilot/will/mynamespaces.ihh>Functions | |
| void | add_apc (core::pose::Pose &pose, core::id::AtomID aid1, core::id::AtomID aid2, core::Real mean, core::Real sd, core::scoring::ScoreType st=core::scoring::atom_pair_constraint) |
| void | add_agc (core::pose::Pose &pose, core::id::AtomID aid1, core::id::AtomID aid2, core::id::AtomID aid3, core::Real mean, core::Real sd) |
| void | minimize (Pose &pose, ScoreFunctionOP sf) |
| void | design (Pose &pose, ScoreFunctionOP sf) |
| void * | doit (void *) |
| int | main (int argc, char *argv[]) |
Variables | |
| static basic::Tracer | TR ("organopv") |
| void add_agc | ( | core::pose::Pose & | pose, |
| core::id::AtomID | aid1, | ||
| core::id::AtomID | aid2, | ||
| core::id::AtomID | aid3, | ||
| core::Real | mean, | ||
| core::Real | sd | ||
| ) |
References basic::options::OptionKeys::ddg::mean, beta_nonlocal::pose, and sd().
| void add_apc | ( | core::pose::Pose & | pose, |
| core::id::AtomID | aid1, | ||
| core::id::AtomID | aid2, | ||
| core::Real | mean, | ||
| core::Real | sd, | ||
| core::scoring::ScoreType | st = core::scoring::atom_pair_constraint |
||
| ) |
References basic::options::OptionKeys::ddg::mean, beta_nonlocal::pose, and sd().
Referenced by doit().
| void design | ( | Pose & | pose, |
| ScoreFunctionOP | sf | ||
| ) |
References beta_nonlocal::pose, basic::options::OptionKeys::casp::repack, basic::options::OptionKeys::out::sf, and vancomycin::task.
Referenced by doit().
| void* doit | ( | void * | ) |
References add_apc(), utility::io::oc::cerr, basic::options::OptionKeys::constraints::constraints, design(), numeric::random::gaussian(), create_a3b_hbs::i, create_a3b_hbs::j, create_a3b_hbs::k, min(), minimize(), option, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, numeric::rotation_matrix_degrees(), basic::options::OptionKeys::out::sf, ObjexxFCL::string_of(), tag, numeric::random::uniform(), and basic::options::OptionKeys::parser::view.
Referenced by main().
| int main | ( | int | argc, |
| char * | argv[] | ||
| ) |
References argv, doit(), test.T009_Exceptions::e, basic::init(), option, basic::options::OptionKeys::parser::view, and viewer_main().
| void minimize | ( | Pose & | pose, |
| ScoreFunctionOP | sf | ||
| ) |
|
static |
1.9.1