util.cc File Reference

Utility methods for protocols/glycan_docking/GlycanDockProtocol. More...

#include <protocols/minimization_packing/MinMover.hh>
#include <protocols/moves/MonteCarlo.hh>
#include <protocols/moves/MoverContainer.hh>
#include <protocols/carbohydrates/RingPlaneFlipMover.hh>
#include <protocols/docking/DockingInitialPerturbation.hh>
#include <protocols/docking/util.hh>
#include <protocols/rigid/RigidBodyMover.hh>
#include <protocols/simple_moves/BackboneMover.hh>
#include <protocols/simple_moves/BBDihedralSamplerMover.hh>
#include <protocols/simple_moves/bb_sampler/SugarBBSampler.hh>
#include <protocols/simple_moves/bb_sampler/SmallBBSampler.hh>
#include <protocols/minimization_packing/PackRotamersMover.hh>
#include <protocols/minimization_packing/RotamerTrialsMover.hh>
#include <protocols/analysis/InterfaceAnalyzerMover.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/simple_metrics/metrics/SelectedResiduesPyMOLMetric.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pack/task/operation/TaskOperations.hh>
#include <core/pack/task/operation/NoRepackDisulfides.hh>
#include <protocols/simple_task_operations/RestrictToInterface.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/carbohydrates/GlycanTreeSet.hh>
#include <core/conformation/carbohydrates/util.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/pose/Pose.hh>
#include <core/pose/PDBInfo.hh>
#include <core/pose/carbohydrates/util.hh>
#include <core/pose/extra_pose_info_util.hh>
#include <core/types.hh>
#include <core/select/util.hh>
#include <core/select/residue_selector/ChainSelector.hh>
#include <core/select/residue_selector/FalseResidueSelector.hh>
#include <core/select/residue_selector/NeighborhoodResidueSelector.hh>
#include <core/select/residue_selector/ReturnResidueSubsetSelector.hh>
#include <core/select/residue_selector/util.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/packing.OptionKeys.gen.hh>
#include <numeric/angle.functions.hh>
#include <numeric/random/random.hh>
#include <utility/pointer/owning_ptr.hh>
#include <utility/string_util.hh>
#include <utility/vector1.hh>
#include <basic/Tracer.hh>
#include <ObjexxFCL/FArray2D.hh>

Namespaces
	protocols
	The instance of Loops contained by AbrelaxApplication should be replaced by a LoopsOP.
	protocols::glycan_docking

Functions
static basic::Tracer	TR ("protocols.glycan_docking.util")
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...

Detailed Description

Utility methods for protocols/glycan_docking/GlycanDockProtocol.

Author

Morgan Nance (morga.nosp@m.nlna.nosp@m.nce@g.nosp@m.mail.nosp@m..com)

Function Documentation

TR()

static basic::Tracer TR ( "protocols.glycan_docking.util"  )

static