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Rosetta
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Utility methods for protocols/glycan_docking/GlycanDockProtocol. More...
#include <protocols/minimization_packing/MinMover.fwd.hh>#include <protocols/moves/MonteCarlo.fwd.hh>#include <protocols/moves/MoverContainer.fwd.hh>#include <protocols/minimization_packing/PackRotamersMover.fwd.hh>#include <protocols/minimization_packing/RotamerTrialsMover.fwd.hh>#include <protocols/analysis/InterfaceAnalyzerMover.fwd.hh>#include <core/scoring/ScoreFunction.fwd.hh>#include <core/pack/task/TaskFactory.fwd.hh>#include <core/kinematics/MoveMap.fwd.hh>#include <core/pose/Pose.fwd.hh>#include <core/types.hh>#include <core/select/residue_selector/ChainSelector.fwd.hh>#include <utility/vector1.hh>#include <ObjexxFCL/FArray2D.fwd.hh>#include <core/conformation/Residue.fwd.hh>Namespaces | |
| protocols | |
| The instance of Loops contained by AbrelaxApplication should be replaced by a LoopsOP. | |
| protocols::glycan_docking | |
Functions | |
| core::select::residue_selector::ChainSelectorCOP | protocols::glycan_docking::setup_glycoligand_selector (std::string const &docking_partners) |
| Creates a ChainSelector based on the downstream partner (glycoligand) More... | |
| utility::vector1< bool > | protocols::glycan_docking::get_glycolig_subset_with_torsions (core::pose::Pose const &pose, core::select::residue_selector::ChainSelectorCOP glycolig_selector) |
| Return a residue subset where carbohydrates of the glycoligand. More... | |
| core::pack::task::TaskFactoryOP | protocols::glycan_docking::setup_GlycanDock_taskfactory (core::Size const docking_jump_num, core::Real const interface_packing_distance, bool const prepack_only) |
| Create a TaskFactory appropriate for the GlycanDockProtocol. More... | |
| core::kinematics::MoveMapOP | protocols::glycan_docking::setup_GlycanDock_movemap (core::pose::Pose const &pose, core::select::residue_selector::ChainSelectorCOP glycolig_selector, bool const lock_rings, core::Size const dock_jump_num) |
| Create a MoveMap appropriate for structure minimization. More... | |
| protocols::moves::SequenceMoverOP | protocols::glycan_docking::setup_GlycanDock_stage1_rb_seqmover (core::pose::Pose const &pose, core::Size const docking_jump_num, core::Real const stage1_rotation_magnitude, core::Real const stage1_translation_magnitude, bool const stage1_rotate_glycolig_about_com) |
| Create SequenceMover holding Stage 1 rigid-body perturbation Movers. More... | |
| protocols::moves::RandomMoverOP | protocols::glycan_docking::setup_GlycanDock_stage2_rb_randmover (core::Size const docking_jump_num, core::Real const stage2_rotation_magnitude, core::Real const stage2_translaation_magnitude, bool const slide_glycolig_into_contact) |
| Create RandomMover holding Stage 2 rigid-body perturbation Movers. More... | |
| protocols::moves::RandomMoverOP | protocols::glycan_docking::setup_GlycanDock_stage2_tor_randmover (core::pose::Pose const &pose, utility::vector1< bool > const &glycolig_subset_with_torsions, core::scoring::ScoreFunctionOP sf, core::Real const mc_kt, core::Size const n_shear_moves, bool const refine_only) |
| Create RandomMover holding Stage 2 torsion angle perturbation Movers. More... | |
| void | protocols::glycan_docking::do_stage1_tor_uniform_perturbation (core::pose::Pose &pose, utility::vector1< bool > const &glycolig_subset, core::Real const stage1_tor_perturb_mag) |
| Apply small uniform perturbation on each glycosidic torsion angle. More... | |
| void | protocols::glycan_docking::do_stage1_conformation_initialization (core::pose::Pose &pose, protocols::moves::SequenceMoverOP stage1_rb_seqmover, utility::vector1< bool > const &glycolig_subset, bool const glycolig_has_dihedrals, core::Real const stage1_tor_perturb_mag) |
| Apply Stage 1 initial conformation perturbation to input Pose. More... | |
| core::Size | protocols::glycan_docking::do_stage2_sample_pack_min_cycle (core::pose::Pose &pose, protocols::moves::RandomMoverOP stage2_mover, core::Size const n_rounds, minimization_packing::PackRotamersMoverOP full_packer, minimization_packing::EnergyCutRotamerTrialsMoverOP ecut_packer, core::Size const full_pack_every_x_rounds, minimization_packing::MinMoverOP min_mover, moves::MonteCarloOP mc) |
| Apply an inner cycle of Stage 2 sampling and optimization. More... | |
| bool | protocols::glycan_docking::calc_res_contact (core::conformation::ResidueCOP rsd_ii, core::conformation::ResidueCOP rsd_jj, core::Real const dist_cutoff) |
| Determine if rsd_ii is in contact with rsd_jj. More... | |
| ObjexxFCL::FArray2D_bool | protocols::glycan_docking::gen_intf_contact_map (core::pose::Pose const &pose, utility::vector1< bool > const &receptor_nbrhood_subset, utility::vector1< bool > const &glycolig_subset, core::Real const dist_cutoff) |
| Generate a map of Pose interface contacts between the. More... | |
| utility::vector1< core::Real > | protocols::glycan_docking::calc_GlycanDock_intf_metrics (core::pose::Pose &pose, core::pose::Pose const &ref_pose, utility::vector1< bool > const &glycolig_subset, core::Real const dist_cutoff=5) |
| Calculate various metrics describing the protein-glycoligand interface. More... | |
| protocols::analysis::InterfaceAnalyzerMoverOP | protocols::glycan_docking::get_GlycanDock_IAM (std::string const &docking_partners, core::scoring::ScoreFunctionOP sf) |
| Create an InterfaceAnalyzerMover appropriate for GlycanDock output. More... | |
Utility methods for protocols/glycan_docking/GlycanDockProtocol.
1.9.1