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Rosetta
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aginsparg, ipatel, sthyme More...
#include <devel/init.hh>#include <core/types.hh>#include <core/chemical/AA.hh>#include <core/chemical/ResidueType.hh>#include <core/chemical/MutableResidueType.hh>#include <core/chemical/ResidueTypeSet.hh>#include <core/chemical/ResidueTypeFinder.hh>#include <core/io/pdb/pdb_writer.hh>#include <basic/options/option.hh>#include <core/pose/Pose.hh>#include <core/scoring/ScoreFunction.hh>#include <core/scoring/ScoreFunctionFactory.hh>#include <core/id/AtomID.hh>#include <core/scoring/dna/setup.hh>#include <protocols/dna/RestrictDesignToProteinDNAInterface.hh>#include <protocols/motifs/LigandMotifSearch.hh>#include <protocols/motifs/LigandMotifSearch.fwd.hh>#include <protocols/motifs/MotifLibrary.hh>#include <core/conformation/Residue.hh>#include <core/conformation/Conformation.hh>#include <core/chemical/ChemicalManager.hh>#include <protocols/motifs/Motif.hh>#include <core/chemical/residue_io.hh>#include <protocols/motifs/MotifHit.hh>#include <core/pack/rotamer_set/RotamerSet.hh>#include <core/pack/rotamer_set/RotamerSetFactory.hh>#include <protocols/motifs/BuildPosition.hh>#include <core/scoring/methods/EnergyMethodOptions.hh>#include <core/kinematics/MoveMap.hh>#include <core/scoring/constraints/CoordinateConstraint.hh>#include <core/scoring/constraints/ConstraintSet.hh>#include <protocols/minimization_packing/MinMover.hh>#include <core/scoring/Energies.hh>#include <core/scoring/EnergyMap.hh>#include <core/scoring/hbonds/HBondSet.hh>#include <core/scoring/hbonds/hbonds.hh>#include <cmath>#include <core/pose/PDBInfo.hh>#include <core/chemical/GlobalResidueTypeSet.hh>#include <protocols/dna/PDBOutput.hh>#include <protocols/dna/util.hh>#include <protocols/motifs/motif_utils.hh>#include <basic/prof.hh>#include <basic/Tracer.hh>#include <core/import_pose/import_pose.hh>#include <core/import_pose/atom_tree_diffs/atom_tree_diff.hh>#include <utility/io/ozstream.hh>#include <utility/file/file_sys_util.hh>#include <utility/file/FileName.hh>#include <utility/vector1.hh>#include <utility/string_util.hh>#include <utility/excn/Exceptions.hh>#include <fstream>#include <iostream>#include <string>#include <queue>#include <functional>#include <basic/options/keys/out.OptionKeys.gen.hh>#include <basic/options/keys/in.OptionKeys.gen.hh>#include <basic/options/keys/score.OptionKeys.gen.hh>#include <basic/options/keys/dna.OptionKeys.gen.hh>#include <basic/options/keys/motifs.OptionKeys.gen.hh>#include <core/pose/xyzStripeHashPose.hh>#include <numeric/geometry/hashing/xyzStripeHash.hh>#include <numeric/geometry/hashing/xyzStripeHash.fwd.hh>#include <numeric/xyzVector.hh>#include <protocols/ligand_docking/InterfaceScoreCalculator.hh>#include <protocols/ligand_docking/ligand_scores.hh>#include <protocols/qsar/scoring_grid/AtrGrid.hh>#include <protocols/qsar/scoring_grid/RepGrid.hh>#include <protocols/qsar/scoring_grid/VdwGrid.hh>#include <protocols/qsar/scoring_grid/HbaGrid.hh>#include <protocols/qsar/scoring_grid/HbdGrid.hh>#include <protocols/qsar/scoring_grid/GridSet.hh>#include <protocols/ligand_docking/MoveMapBuilder.hh>#include <protocols/ligand_docking/LigandArea.hh>#include <protocols/ligand_docking/InterfaceBuilder.hh>#include <protocols/ligand_docking/MoveMapBuilder.fwd.hh>#include <core/optimization/MinimizerOptions.hh>#include <protocols/ligand_docking/LigandBaseProtocol.hh>#include <protocols/ligand_docking/HighResDocker.hh>#include <protocols/ligand_docking/LigandDockProtocol.hh>#include <protocols/ligand_docking/ligand_dock_impl.hh>#include <core/scoring/func/HarmonicFunc.hh>#include <core/chemical/PoseResidueTypeSet.hh>#include <ObjexxFCL/FArray1D.hh>#include <time.h>#include <typeinfo>Functions | |
| int | main (int argc, char *argv[]) |
Variables | |
| static basic::Tracer | TR ("apps.pilot.motif_dna_packer_design") |
aginsparg, ipatel, sthyme
| int main | ( | int | argc, |
| char * | argv[] | ||
| ) |
References argv, utility::io::oc::cerr, utility::io::oc::cout, test.T009_Exceptions::e, utility::file::file_exists(), lactamize::filename, run_backbone::float, basic::init(), in::file::l(), basic::options::OptionKeys::in::file::list, ms_tr, natoms(), option, predPRE::pdbname, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, basic::prof_reset(), cal_NBR_radius::res_num, basic::options::OptionKeys::motifs::resolution_scale_factor, in::file::s(), utility::string_split(), basic::t_info, basic::options::OptionKeys::inout::dbms::user, x, numeric::xyzVector< T >::x(), basic::options::OptionKeys::motifs::x_max_holes, basic::options::OptionKeys::motifs::x_min_holes, predPRE::y, numeric::xyzVector< T >::y(), basic::options::OptionKeys::motifs::y_max_holes, basic::options::OptionKeys::motifs::y_min_holes, predPRE::z, numeric::xyzVector< T >::z(), basic::options::OptionKeys::motifs::z_max_holes, and basic::options::OptionKeys::motifs::z_min_holes.
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1.9.1