|
Rosetta
|
All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Properties Friends Macros Pages
|
Rosetta
|
#include <protocols/farna/util.hh>#include <core/pose/rna/RNA_IdealCoord.hh>#include <protocols/stepwise/modeler/rna/util.hh>#include <protocols/stepwise/modeler/output_util.hh>#include <core/types.hh>#include <core/chemical/AA.hh>#include <core/chemical/AtomType.hh>#include <core/chemical/ChemicalManager.hh>#include <core/chemical/ResidueTypeSet.hh>#include <core/chemical/util.hh>#include <core/chemical/VariantType.hh>#include <core/conformation/ResidueFactory.hh>#include <core/conformation/Residue.hh>#include <core/conformation/Conformation.hh>#include <core/scoring/ScoringManager.hh>#include <core/scoring/ScoreFunctionFactory.hh>#include <core/sequence/util.hh>#include <core/sequence/Sequence.hh>#include <core/init/init.hh>#include <core/optimization/AtomTreeMinimizer.hh>#include <core/optimization/MinimizerOptions.hh>#include <basic/options/option.hh>#include <basic/options/keys/OptionKeys.hh>#include <basic/options/util.hh>#include <basic/options/option_macros.hh>#include <protocols/viewer/viewers.hh>#include <core/id/AtomID.hh>#include <core/id/NamedAtomID.hh>#include <core/pose/Pose.hh>#include <core/pose/util.hh>#include <core/pose/full_model_info/util.hh>#include <core/pose/full_model_info/FullModelInfo.hh>#include <core/scoring/rms_util.tmpl.hh>#include <core/scoring/ScoreFunction.hh>#include <core/scoring/ScoreType.hh>#include <core/scoring/rna/RNA_TorsionPotential.hh>#include <core/pose/rna/util.hh>#include <core/chemical/rna/util.hh>#include <core/io/silent/SilentFileData.fwd.hh>#include <core/io/silent/SilentFileData.hh>#include <core/io/silent/BinarySilentStruct.hh>#include <core/import_pose/import_pose.hh>#include <core/pose/annotated_sequence.hh>#include <core/scoring/EnergyGraph.hh>#include <core/scoring/Energies.hh>#include <core/scoring/EnergyMap.hh>#include <core/kinematics/FoldTree.hh>#include <core/kinematics/AtomTree.hh>#include <core/kinematics/Jump.hh>#include <core/kinematics/MoveMap.hh>#include <core/pack/rotamer_trials.hh>#include <core/pack/pack_rotamers.hh>#include <core/pack/task/PackerTask.hh>#include <core/pack/task/TaskFactory.hh>#include <core/pack/rotamer_set/RotamerCouplings.hh>#include <core/pack/rotamer_set/WaterAnchorInfo.hh>#include <core/pack/rotamer_set/WaterPackingInfo.hh>#include <core/pack/rotamer_set/WaterPackingInfo.fwd.hh>#include <protocols/moves/Mover.hh>#include <protocols/moves/Mover.fwd.hh>#include <core/scoring/constraints/Constraint.hh>#include <core/scoring/constraints/ConstraintIO.hh>#include <core/scoring/constraints/ConstraintSet.hh>#include <core/scoring/constraints/ConstraintSet.fwd.hh>#include <core/scoring/constraints/CoordinateConstraint.hh>#include <core/scoring/constraints/AtomPairConstraint.hh>#include <core/scoring/constraints/AngleConstraint.hh>#include <core/scoring/func/HarmonicFunc.hh>#include <core/scoring/constraints/util.hh>#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/edensity.OptionKeys.gen.hh>#include <basic/options/keys/rna.OptionKeys.gen.hh>#include <core/pose/PDBInfo.hh>#include <core/chemical/rna/RNA_FittedTorsionInfo.hh>#include <utility/vector1.hh>#include <utility/io/ozstream.hh>#include <utility/io/izstream.hh>#include <numeric/conversions.hh>#include <numeric/xyz.functions.hh>#include <iostream>#include <string>#include <utility/excn/Exceptions.hh>Go to the source code of this file.
Functions | |
| bool | check_num_in_vector (int input_num, utility::vector1< int > const &input_vector) |
| void | translate_residue (conformation::Residue &rsd, Vector const &nbr_atom_xyz) |
| bool | check_in_bonded_list (core::id::AtomID const &atom_id1, core::id::AtomID const &atom_id2, utility::vector1< std::pair< core::id::AtomID, core::id::AtomID > > &bonded_atom_list) |
| bool | check_in_bond_angle_list (core::id::AtomID const &atom_id1, core::id::AtomID const &atom_id2, core::id::AtomID const &atom_id3, utility::vector1< std::pair< core::id::AtomID, std::pair< core::id::AtomID, core::id::AtomID > > > &bond_angle_list) |
| void | apply_ideal_coordinates (pose::Pose const &pose, pose::Pose &pose_reference) |
| void | add_bond_constraint (core::id::AtomID const &atom_id1, core::id::AtomID const &atom_id2, utility::vector1< std::pair< core::id::AtomID, core::id::AtomID > > &bonded_atom_list, core::pose::Pose const &pose, core::pose::Pose const &pose_reference, core::scoring::constraints::ConstraintSetOP &cst_set) |
| void | add_bond_angle_constraint (core::id::AtomID const &atom_id1, core::id::AtomID const &atom_id2, core::id::AtomID const &atom_id3, utility::vector1< std::pair< core::id::AtomID, std::pair< core::id::AtomID, core::id::AtomID > > > &bond_angle_list, core::pose::Pose const &pose, core::pose::Pose const &pose_reference, core::scoring::constraints::ConstraintSetOP &cst_set) |
| bool | check_if_really_connected (core::pose::Pose const &pose, core::id::AtomID const &atom_id1, core::id::AtomID const &atom_id2) |
| bool | i_want_this_atom_to_move (conformation::Residue const &residue2, Size const &k) |
| bool | i_want_this_atom_to_move (pose::Pose const &pose, core::id::AtomID const &atom_id) |
| bool | is_atom_exist_in_reference (pose::Pose const &pose, pose::Pose const &pose_reference, core::id::AtomID const &atom_id) |
| void | create_pose_reference (pose::Pose const &pose, pose::Pose &pose_reference) |
| void | vary_bond_geometry (core::kinematics::MoveMap &mm, pose::Pose &pose, pose::Pose const &pose_reference, ObjexxFCL::FArray1D< bool > &allow_insert_) |
| int | add_virtual_res (core::pose::Pose &pose) |
| void | setup_fold_tree (pose::Pose &pose, utility::vector1< core::Size > const &cutpoint_list) |
| bool | is_elem_in_list (core::Size const elem, utility::vector1< core::Size > const &list) |
| void | setup_fold_tree_sample_res (pose::Pose &pose, utility::vector1< core::Size > const &sample_res_list) |
| void | pyrimidine_flip_trial (pose::Pose &pose, utility::vector1< Size > const &fixed_res_list, scoring::ScoreFunctionOP scorefxn) |
| void | pdb_minimizer () |
| void * | my_main (void *) |
| int | main (int argc, char *argv[]) |
| void add_bond_angle_constraint | ( | core::id::AtomID const & | atom_id1, |
| core::id::AtomID const & | atom_id2, | ||
| core::id::AtomID const & | atom_id3, | ||
| utility::vector1< std::pair< core::id::AtomID, std::pair< core::id::AtomID, core::id::AtomID > > > & | bond_angle_list, | ||
| core::pose::Pose const & | pose, | ||
| core::pose::Pose const & | pose_reference, | ||
| core::scoring::constraints::ConstraintSetOP & | cst_set | ||
| ) |
Definition at line 251 of file erraser_minimizer.cc.
References numeric::angle_radians(), check_in_bond_angle_list(), app.surface_docking.surface_docking::constraints, utility::io::oc::cout, numeric::conversions::degrees(), has, numeric::conversions::radians(), and numeric::crick_equations::xyz().
Referenced by vary_bond_geometry().
| void add_bond_constraint | ( | core::id::AtomID const & | atom_id1, |
| core::id::AtomID const & | atom_id2, | ||
| utility::vector1< std::pair< core::id::AtomID, core::id::AtomID > > & | bonded_atom_list, | ||
| core::pose::Pose const & | pose, | ||
| core::pose::Pose const & | pose_reference, | ||
| core::scoring::constraints::ConstraintSetOP & | cst_set | ||
| ) |
Definition at line 214 of file erraser_minimizer.cc.
References check_in_bonded_list(), app.surface_docking.surface_docking::constraints, utility::io::oc::cout, has, make_symmdef_file_denovo::length, and numeric::crick_equations::xyz().
Referenced by vary_bond_geometry().
| int add_virtual_res | ( | core::pose::Pose & | pose | ) |
Definition at line 523 of file erraser_minimizer.cc.
References utility::io::oc::cout, and clean_pdb_keep_ligand::nres.
Referenced by nucleobase_probe_score_test(), and pdb_minimizer().
| void apply_ideal_coordinates | ( | pose::Pose const & | pose, |
| pose::Pose & | pose_reference | ||
| ) |
Definition at line 187 of file erraser_minimizer.cc.
References option.
Referenced by create_pose_reference().
| bool check_if_really_connected | ( | core::pose::Pose const & | pose, |
| core::id::AtomID const & | atom_id1, | ||
| core::id::AtomID const & | atom_id2 | ||
| ) |
Definition at line 305 of file erraser_minimizer.cc.
References test.T220_AtomAtomPairEnergies::atom1, and test.T220_AtomAtomPairEnergies::atom2.
Referenced by vary_bond_geometry().
| bool check_in_bond_angle_list | ( | core::id::AtomID const & | atom_id1, |
| core::id::AtomID const & | atom_id2, | ||
| core::id::AtomID const & | atom_id3, | ||
| utility::vector1< std::pair< core::id::AtomID, std::pair< core::id::AtomID, core::id::AtomID > > > & | bond_angle_list | ||
| ) |
Definition at line 171 of file erraser_minimizer.cc.
References assign_charges::first.
Referenced by add_bond_angle_constraint().
| bool check_in_bonded_list | ( | core::id::AtomID const & | atom_id1, |
| core::id::AtomID const & | atom_id2, | ||
| utility::vector1< std::pair< core::id::AtomID, core::id::AtomID > > & | bonded_atom_list | ||
| ) |
Definition at line 156 of file erraser_minimizer.cc.
References assign_charges::first.
Referenced by add_bond_constraint().
| bool check_num_in_vector | ( | int | input_num, |
| utility::vector1< int > const & | input_vector | ||
| ) |
Definition at line 138 of file erraser_minimizer.cc.
Referenced by pdb_minimizer(), and pyrimidine_flip_trial().
| void create_pose_reference | ( | pose::Pose const & | pose, |
| pose::Pose & | pose_reference | ||
| ) |
Definition at line 354 of file erraser_minimizer.cc.
References apply_ideal_coordinates().
Referenced by pdb_minimizer().
| bool i_want_this_atom_to_move | ( | conformation::Residue const & | residue2, |
| Size const & | k | ||
| ) |
Definition at line 323 of file erraser_minimizer.cc.
Referenced by i_want_this_atom_to_move(), and vary_bond_geometry().
| bool i_want_this_atom_to_move | ( | pose::Pose const & | pose, |
| core::id::AtomID const & | atom_id | ||
| ) |
Definition at line 336 of file erraser_minimizer.cc.
References i_want_this_atom_to_move().
| bool is_atom_exist_in_reference | ( | pose::Pose const & | pose, |
| pose::Pose const & | pose_reference, | ||
| core::id::AtomID const & | atom_id | ||
| ) |
Definition at line 342 of file erraser_minimizer.cc.
References utility::io::oc::cout, and has.
Referenced by vary_bond_geometry().
| bool is_elem_in_list | ( | core::Size const | elem, |
| utility::vector1< core::Size > const & | list | ||
| ) |
Definition at line 572 of file erraser_minimizer.cc.
Referenced by setup_fold_tree_sample_res().
Definition at line 920 of file erraser_minimizer.cc.
References utility::io::oc::cout, basic::init(), utility::excn::EXCN_Base::msg(), my_main(), and NEW_OPT.
| void* my_main | ( | void * | ) |
Definition at line 913 of file erraser_minimizer.cc.
References utility::options::OptionKeys::options::exit, and pdb_minimizer().
Referenced by main().
| void pdb_minimizer | ( | ) |
Definition at line 644 of file erraser_minimizer.cc.
References add_virtual_res(), check_num_in_vector(), app.surface_docking.surface_docking::constraints, utility::io::oc::cout, create_pose_reference(), demo.D030_Fold_tree::fold_tree(), test.T200_Scoring::ii, max(), min(), app.delta_score_per_mutation::mm, ContactMap::native, clean_pdb_keep_ligand::nres, option, app.surface_docking.surface_docking::pose, pyrimidine_flip_trial(), test.G100_Functions_Input::score, PyMOL_demo::scorefxn, setup_fold_tree(), show(), app.surface_docking.surface_docking::start_pose, utility::options::OptionKeys::options::user, utility_exit_with_message, vary_bond_geometry(), and test.T200_Scoring::weights.
Referenced by my_main().
| void pyrimidine_flip_trial | ( | pose::Pose & | pose, |
| utility::vector1< Size > const & | fixed_res_list, | ||
| scoring::ScoreFunctionOP | scorefxn | ||
| ) |
Definition at line 606 of file erraser_minimizer.cc.
References check_num_in_vector(), utility::io::oc::cout, test.Workshop4test::new_score, app.surface_docking.surface_docking::pose, and app.delta_score_per_mutation::res.
Referenced by pdb_minimizer().
| void setup_fold_tree | ( | pose::Pose & | pose, |
| utility::vector1< core::Size > const & | cutpoint_list | ||
| ) |
Definition at line 548 of file erraser_minimizer.cc.
References demo.D060_Folding::f, and clean_pdb_keep_ligand::nres.
Referenced by pdb_minimizer().
| void setup_fold_tree_sample_res | ( | pose::Pose & | pose, |
| utility::vector1< core::Size > const & | sample_res_list | ||
| ) |
Definition at line 581 of file erraser_minimizer.cc.
References demo.D060_Folding::f, is_elem_in_list(), and clean_pdb_keep_ligand::nres.
| void translate_residue | ( | conformation::Residue & | rsd, |
| Vector const & | nbr_atom_xyz | ||
| ) |
Definition at line 146 of file erraser_minimizer.cc.
| void vary_bond_geometry | ( | core::kinematics::MoveMap & | mm, |
| pose::Pose & | pose, | ||
| pose::Pose const & | pose_reference, | ||
| ObjexxFCL::FArray1D< bool > & | allow_insert_ | ||
| ) |
Definition at line 367 of file erraser_minimizer.cc.
References add_bond_angle_constraint(), add_bond_constraint(), check_if_really_connected(), app.surface_docking.surface_docking::constraints, utility::io::oc::cout, i_want_this_atom_to_move(), is_atom_exist_in_reference(), clean_pdb_keep_ligand::nres, and test.Workshop4test::PHI.
Referenced by pdb_minimizer().
1.8.7