Given a set of cut1/cut2/cut3/cut4 distance specifications, alter a packing task to set residues within alpha carbons within cut1 of a ligand (or within cut2 with beta carbons facing inwards) to redesign, and within cut3 (or cut4 facing inwards) to repack, and all others to fixed. If a resfile is provided, only do the detection for those residues set to AUTO in the resfile. More...

#include <EnzdesTaskOperations.hh>

Inheritance diagram for protocols::enzdes::DetectProteinLigandInterface:

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Collaboration diagram for protocols::enzdes::DetectProteinLigandInterface:

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Public Types
typedef core::pack::task::operation::TaskOperationOP	TaskOperationOP

typedef core::pose::Pose	Pose

typedef core::pack::task::PackerTask	PackerTask

Public Types inherited from core::pack::task::operation::TaskOperation
typedef utility::tag::TagPtr	TagPtr

typedef pose::Pose	Pose

Public Member Functions
	DetectProteinLigandInterface ()

	~DetectProteinLigandInterface ()

virtual TaskOperationOP	clone () const
	Create another task operation of the type matching the most-derived version of the class. More...

void	init_from_options ()
	Initialize the class based on the command line options. More...

virtual void	apply (Pose const &pose, PackerTask &task) const
	Change a packer task in some way. The input pose is the one to which the input task will be later applied. More...

virtual void	parse_tag (TagPtr)
	Used to parse an xml-like tag to load parameters and properties. More...

void	find_design_interface (core::pose::Pose const &pose, std::set< core::Size > const &interface_target_res, core::Real cut1, core::Real cut2, core::Real cut3, core::Real cut4, utility::vector1< bool > &repack_res, utility::vector1< bool > &design_res) const

void	find_design_interface_arg_sweep (core::pose::Pose const &pose, std::set< core::Size > const &interface_target_res, core::Real cut1, core::Real cut2, core::Real cut3, core::Real cut4, core::Real arg_sweep_cutoff, utility::vector1< bool > &repack_res, utility::vector1< bool > &design_res) const

bool	get_design () const

void	set_design (bool const design_in)

bool	get_no_design_cys () const

void	set_no_design_cys (bool const no_design_cys_in)

void	set_design_target_res (std::set< core::Size > const &target_res)

Public Member Functions inherited from core::pack::task::operation::TaskOperation
virtual	~TaskOperation ()

virtual void	parse_def (utility::lua::LuaObject const &def)

Static Public Member Functions
static void	register_options ()

static void	add_observer_cache_segments_to_set (core::pose::Pose const &pose, std::set< core::Size > &set)

Private Attributes
bool	detect_design_interface_
	Control whether the detect design interface algorithm is run. More...

bool	arg_sweep_interface_
	Use protein-DNA interface like arginine rotamer sweep to identify designable positions. More...

core::Real	arg_sweep_cutoff_
	Dicitate the max distance from arginine to ligand for position to be counted as designable. More...

bool	catalytic_res_part_of_interface_
	interface can be declared as all catalytic res More...

bool	design_
	Depending on the design_ variable setting the cut1 and cut2 can be turned off and no design will take place. More...

bool	repack_only_
	Turn of design (repack_only_), or repacking and design (score_only_) More...

bool	score_only_

core::Real	cut1_
	cut1_ through cut4_ define the shells over which the interface detection takes place More...

core::Real	cut2_

core::Real	cut3_

core::Real	cut4_

std::string	resfilename_
	If resfilename_ is not empty, load it and obey the AUTO directives therein. More...

std::set< core::Size >	design_target_res_

bool	add_observer_cache_segs_to_interface_

bool	no_design_cys_
	Should we prohibit designing to non disulfide cys? More...

bool	catres_only_

bool	use_cstid_list_

std::string	cstid_list_

Detailed Description

Given a set of cut1/cut2/cut3/cut4 distance specifications, alter a packing task to set residues within alpha carbons within cut1 of a ligand (or within cut2 with beta carbons facing inwards) to redesign, and within cut3 (or cut4 facing inwards) to repack, and all others to fixed. If a resfile is provided, only do the detection for those residues set to AUTO in the resfile.

Definition at line 74 of file EnzdesTaskOperations.hh.

Member Typedef Documentation

typedef core::pack::task::PackerTask protocols::enzdes::DetectProteinLigandInterface::PackerTask

Definition at line 80 of file EnzdesTaskOperations.hh.

typedef core::pose::Pose protocols::enzdes::DetectProteinLigandInterface::Pose

Definition at line 79 of file EnzdesTaskOperations.hh.

typedef core::pack::task::operation::TaskOperationOP protocols::enzdes::DetectProteinLigandInterface::TaskOperationOP

Definition at line 78 of file EnzdesTaskOperations.hh.

Constructor & Destructor Documentation

protocols::enzdes::DetectProteinLigandInterface::DetectProteinLigandInterface ( )

Definition at line 203 of file EnzdesTaskOperations.cc.

References design_target_res_, and init_from_options().

Referenced by clone().

protocols::enzdes::DetectProteinLigandInterface::~DetectProteinLigandInterface ( )

Definition at line 217 of file EnzdesTaskOperations.cc.

Member Function Documentation

void protocols::enzdes::DetectProteinLigandInterface::add_observer_cache_segments_to_set	(	core::pose::Pose const &	pose,
		std::set< core::Size > &	set
	)

static

Definition at line 700 of file EnzdesTaskOperations.cc.

References core::pose::Pose::observer_cache(), and core::pose::datacache::CacheableObserverType::SPECIAL_SEGMENTS_OBSERVER.

Referenced by protocols::enzdes::BackboneSampler::apply(), and apply().

void protocols::enzdes::DetectProteinLigandInterface::apply	(	Pose const &	pose,
		PackerTask &	task
	)		const

virtual

Change a packer task in some way. The input pose is the one to which the input task will be later applied.

Implements core::pack::task::operation::TaskOperation.

Definition at line 271 of file EnzdesTaskOperations.cc.

References core::conformation::Residue::aa(), core::chemical::aa_cys, add_observer_cache_segments_to_set(), add_observer_cache_segs_to_interface_, core::pack::task::operation::ReadResfileAndObeyLengthEvents::apply(), arg_sweep_cutoff_, arg_sweep_interface_, catalytic_res_part_of_interface_, catres_only_, core::pose::Pose::conformation(), cstid_list_, cut1_, cut2_, cut3_, cut4_, design_, core::pack::task::PackerTask::design_residue(), design_target_res_, detect_design_interface_, core::chemical::DISULFIDE, core::kinematics::FoldTree::downstream_jump_residue(), find_design_interface(), find_design_interface_arg_sweep(), core::pose::Pose::fold_tree(), core::conformation::symmetry::get_asymm_unit_fold_tree(), core::pack::dunbrack::RotamerLibrary::get_instance(), protocols::enzdes::enzutil::get_resnum_from_cstid_list(), core::pack::dunbrack::RotamerLibrary::get_rsd_library(), core::pack::task::ResidueLevelTask::has_behavior(), core::conformation::Residue::has_variant_type(), protocols::enzdes::enzutil::is_catalytic_seqpos(), core::chemical::ResidueType::is_ligand(), core::conformation::Residue::is_ligand(), core::pose::symmetry::is_symmetric(), no_design_cys_, core::pack::task::PackerTask::nonconst_residue_task(), core::chemical::num_canonical_aas, core::kinematics::FoldTree::num_jump(), core::pose::Pose::num_jump(), core::pack::task::PackerTask::pack_residue(), core::pack::task::ResidueLevelTask::prevent_repacking(), repack_only_, core::pack::task::PackerTask::request_symmetrize_by_union(), resfilename_, core::pose::Pose::residue(), core::pack::task::PackerTask::residue_task(), core::pose::Pose::residue_type(), core::pack::task::ResidueLevelTask::restrict_absent_canonical_aas(), core::pack::task::ResidueLevelTask::restrict_to_repacking(), score_only_, core::pose::Pose::total_residue(), protocols::enzdes::tr(), and use_cstid_list_.

core::pack::task::operation::TaskOperationOP protocols::enzdes::DetectProteinLigandInterface::clone ( ) const

virtual

Create another task operation of the type matching the most-derived version of the class.

Implements core::pack::task::operation::TaskOperation.

Definition at line 220 of file EnzdesTaskOperations.cc.

References DetectProteinLigandInterface().

void protocols::enzdes::DetectProteinLigandInterface::find_design_interface	(	core::pose::Pose const &	pose,
		std::set< core::Size > const &	interface_target_res,
		core::Real	cut1,
		core::Real	cut2,
		core::Real	cut3,
		core::Real	cut4,
		utility::vector1< bool > &	repack_res,
		utility::vector1< bool > &	design_res
	)		const

Definition at line 430 of file EnzdesTaskOperations.cc.

References core::conformation::Residue::first_sidechain_atom(), core::conformation::Residue::has(), core::conformation::Residue::is_protein(), core::conformation::Residue::nheavyatoms(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), protocols::enzdes::tr(), and core::conformation::Residue::xyz().

Referenced by apply().

void protocols::enzdes::DetectProteinLigandInterface::find_design_interface_arg_sweep	(	core::pose::Pose const &	pose,
		std::set< core::Size > const &	interface_target_res,
		core::Real	cut1,
		core::Real	cut2,
		core::Real	cut3,
		core::Real	cut4,
		core::Real	arg_sweep_cutoff,
		utility::vector1< bool > &	repack_res,
		utility::vector1< bool > &	design_res
	)		const