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>

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

typedef core::pose::Pose	Pose

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

Public Member Functions
	DetectProteinLigandInterface ()

	~DetectProteinLigandInterface ()

virtual TaskOperationOP	clone () const

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 (TagCOP, DataMap &)

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)

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.

Member Typedef Documentation

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

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

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

Constructor & Destructor Documentation

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

References design_target_res_, and init_from_options().

Referenced by clone().

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

Member Function Documentation

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

static

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

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.

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

virtual

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

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

References numeric::xyzVector< class >::distance_squared(), core::conformation::Residue::first_sidechain_atom(), core::conformation::Residue::has(), core::conformation::Residue::is_protein(), core::conformation::Residue::nheavyatoms(), core::pose::Pose::residue(), utility::to_string(), 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