protocols::glycan_docking Namespace Reference

Classes
class	GlycanDockProtocol
	TODO. More...
class	GlycanDockProtocolCreator

Typedefs
typedef utility::pointer::shared_ptr< GlycanDockProtocol >	GlycanDockProtocolOP
typedef utility::pointer::shared_ptr< GlycanDockProtocol const >	GlycanDockProtocolCOP

Functions
std::ostream &	operator<< (std::ostream &os, GlycanDockProtocol const &mover)
core::select::residue_selector::ChainSelectorCOP	setup_glycoligand_selector (std::string const &docking_partners)
	Creates a ChainSelector based on the downstream partner (glycoligand) More...
utility::vector1< bool >	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	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	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	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	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	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	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	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	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	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	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 >	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	get_GlycanDock_IAM (std::string const &docking_partners, core::scoring::ScoreFunctionOP sf)
	Create an InterfaceAnalyzerMover appropriate for GlycanDock output. More...

Typedef Documentation

GlycanDockProtocolCOP

typedef utility::pointer::shared_ptr< GlycanDockProtocol const > protocols::glycan_docking::GlycanDockProtocolCOP

GlycanDockProtocolOP

typedef utility::pointer::shared_ptr< GlycanDockProtocol > protocols::glycan_docking::GlycanDockProtocolOP

Function Documentation

calc_GlycanDock_intf_metrics()

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.

The return vector1 looks like so:

< num intf res, num intf res in the ref pose,

the fraction of ref pose intf res recovered in the decoy,

num intf contacts, num intf contacts in the ref pose,

the fraction of ref pose intf contacts recovered in the decoy >

References core::select::residue_selector::NeighborhoodResidueSelector::apply(), core::select::residue_selector::count_selected(), gen_intf_contact_map(), core::pose::Pose::pdb_info(), core::select::residue_selector::NeighborhoodResidueSelector::set_distance(), core::select::residue_selector::NeighborhoodResidueSelector::set_focus(), core::select::residue_selector::NeighborhoodResidueSelector::set_include_focus_in_subset(), core::pose::Pose::size(), and protocols::TR().

Referenced by protocols::glycan_docking::GlycanDockProtocol::record_pose_metrics().

calc_res_contact()

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.

If any non-hydrogen atom of rsd_ii is within dist_cutoff

(generally 5 Ang) of any non-hydrogen atom of rsd_jj,

then the two residues are considered contacting

Note

This does not check if an atom is virtual, but virtual

carbohydrate atoms should track their corresponding real atom

Referenced by gen_intf_contact_map().

do_stage1_conformation_initialization()

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.

Note

Stage 1 serves to increase the conformational diversity of

a docking trajectory by injecting a little initial randomness

References do_stage1_tor_uniform_perturbation(), and protocols::TR().

Referenced by protocols::glycan_docking::GlycanDockProtocol::apply().

do_stage1_tor_uniform_perturbation()

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.

Note

Stage 1 serves to increase the conformational diversity of

a docking trajectory by injecting a little initial randomness

References core::pose::Pose::omega(), core::pose::Pose::phi(), core::pose::Pose::psi(), protocols::rigid::random, core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), and core::pose::Pose::set_psi().

Referenced by do_stage1_conformation_initialization().

do_stage2_sample_pack_min_cycle()

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.

Note

Stage 2 is the main docking refinement portion of GlycanDock

References protocols::moves::MS_SUCCESS, and protocols::TR().

Referenced by protocols::glycan_docking::GlycanDockProtocol::perform_stage2_docking_and_optimization().

gen_intf_contact_map()

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.

receptor_nbrhood_subset and the glycolig_subset

receptor_nbrhood_subset: A pre-filtered residue subset

of protein receptor residues at the interface based on

a cutoff of 10 Ang (using the tenA energy map)

glycolig_subset: Subset indicating the carbohydrate

residues of the glycoligand

References calc_res_contact(), and core::pose::Pose::residue().

Referenced by calc_GlycanDock_intf_metrics().

get_GlycanDock_IAM()

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.

get_glycolig_subset_with_torsions()

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.

that have (movable) glycosidic torsion angles

Note

Reducing end carbohydrate does not have dihedrals

References core::pose::carbohydrates::get_n_glycosidic_torsions_in_res(), core::pose::Pose::glycan_tree_set(), core::conformation::Residue::is_carbohydrate(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), core::id::to_string(), core::pose::Pose::total_residue(), and protocols::TR().

Referenced by protocols::glycan_docking::GlycanDockProtocol::apply().

operator<<()

std::ostream & protocols::glycan_docking::operator<<	(	std::ostream &	os,
		GlycanDockProtocol const &	mover
	)

References protocols::glycan_docking::GlycanDockProtocol::show().

setup_GlycanDock_movemap()

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.

Note

Not affected by -prepack_only because minimization is not used

References core::pose::carbohydrates::create_glycan_movemap_from_residue_selector(), core::conformation::Residue::is_branch_point(), core::conformation::Residue::is_carbohydrate(), core::pose::Pose::residue(), core::pose::carbohydrates::set_glycan_iupac_chi_torsions(), core::pose::Pose::size(), and protocols::TR().

Referenced by protocols::glycan_docking::GlycanDockProtocol::apply().

setup_GlycanDock_stage1_rb_seqmover()

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.

References protocols::rigid::partner_downstream, and protocols::TR().

Referenced by protocols::glycan_docking::GlycanDockProtocol::apply().

setup_GlycanDock_stage2_rb_randmover()

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_translation_magnitude,
		bool const	slide_glycolig_into_contact
	)

Create RandomMover holding Stage 2 rigid-body perturbation Movers.

References protocols::moves::MoverContainer::add_mover(), protocols::rigid::partner_downstream, and protocols::TR().

Referenced by protocols::glycan_docking::GlycanDockProtocol::apply().

setup_GlycanDock_stage2_tor_randmover()

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.

References core::pose::Pose::conformation(), core::conformation::carbohydrates::get_n_glycosidic_torsions_in_res(), core::id::omega_dihedral, core::id::phi_dihedral, core::id::psi_dihedral, core::pose::Pose::total_residue(), and protocols::TR().

Referenced by protocols::glycan_docking::GlycanDockProtocol::apply().

setup_GlycanDock_taskfactory()

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.

Note

If -prepack_only is true, TaskFactory is not restricted to interface

References protocols::TR().

Referenced by protocols::glycan_docking::GlycanDockProtocol::apply().

setup_glycoligand_selector()

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)

of the -docking:partners (e.g. AB_X) after some quality assurance

References protocols::docking::comma_separated_partner_chains(), and protocols::TR().

Referenced by protocols::glycan_docking::GlycanDockProtocol::apply().