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:

[legend]

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::TagCOP	TagCOP

typedef basic::datacache::DataMap	DataMap

typedef pose::Pose	Pose

Public Member Functions
	DetectProteinLigandInterface ()

	~DetectProteinLigandInterface () override

TaskOperationOP	clone () const override
	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...

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

void	parse_tag (TagCOP, DataMap &) override
	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_detect_interface () const

void	set_detect_interface (bool setting)

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
	~TaskOperation () override

virtual void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const
	Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More...

Static Public Member Functions
static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

static std::string	keyname ()

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

◆ PackerTask

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

◆ Pose

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

◆ TaskOperationOP

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

Constructor & Destructor Documentation

◆ DetectProteinLigandInterface()

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

References design_target_res_, and init_from_options().

◆ ~DetectProteinLigandInterface()

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

overridedefault

Member Function Documentation

◆ add_observer_cache_segments_to_set()

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(), and core::pose::datacache::SPECIAL_SEGMENTS_OBSERVER.

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

◆ apply()

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

overridevirtual

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.

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(), protocols::enzdes::enzutil::get_resnum_from_cstid_list(), 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::size(), protocols::enzdes::tr(), and use_cstid_list_.

◆ clone()

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

overridevirtual

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

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

◆ find_design_interface()

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 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::size(), core::id::to_string(), protocols::enzdes::tr(), and core::conformation::Residue::xyz().

Referenced by apply().

◆ find_design_interface_arg_sweep()

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

References protocols::dna::argrot_dna_dis2(), protocols::dna::close_to_dna(), 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::size(), core::id::to_string(), protocols::enzdes::tr(), and core::conformation::Residue::xyz().

Referenced by apply().

◆ get_design()

bool protocols::enzdes::DetectProteinLigandInterface::get_design ( ) const

inline

References design_.

◆ get_detect_interface()

bool protocols::enzdes::DetectProteinLigandInterface::get_detect_interface ( ) const

inline

References detect_design_interface_.

◆ get_no_design_cys()

bool protocols::enzdes::DetectProteinLigandInterface::get_no_design_cys ( ) const

inline

References no_design_cys_.

◆ init_from_options()

void protocols::enzdes::DetectProteinLigandInterface::init_from_options ( )

Initialize the class based on the command line options.

References arg_sweep_cutoff_, arg_sweep_interface_, cut1_, cut2_, cut3_, cut4_, detect_design_interface_, repack_only_, resfilename_, and score_only_.

Referenced by DetectProteinLigandInterface(), and protocols::enzdes::ProteinLigandInterfaceUpweighter::ProteinLigandInterfaceUpweighter().

◆ keyname()

static std::string protocols::enzdes::DetectProteinLigandInterface::keyname ( )

inlinestatic

Referenced by protocols::enzdes::DetectProteinLigandInterfaceOperationCreator::keyname(), provide_xml_schema(), protocols::enzdes::ProteinLigandInterfaceUpweighter::provide_xml_schema(), protocols::enzdes::AddRigidBodyLigandConfs::provide_xml_schema(), and protocols::enzdes::AddLigandMotifRotamers::provide_xml_schema().

◆ parse_tag()

void protocols::enzdes::DetectProteinLigandInterface::parse_tag	(	TagCOP	tag,
		DataMap &
	)

overridevirtual

Used to parse an xml-like tag to load parameters and properties.

Reimplemented from core::pack::task::operation::TaskOperation.

References add_observer_cache_segs_to_interface_, arg_sweep_cutoff_, arg_sweep_interface_, catalytic_res_part_of_interface_, catres_only_, cstid_list_, cut1_, cut2_, cut3_, cut4_, design_, detect_design_interface_, no_design_cys_, repack_only_, resfilename_, score_only_, and use_cstid_list_.

◆ provide_xml_schema()

void protocols::enzdes::DetectProteinLigandInterface::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References keyname(), and core::pack::task::operation::task_op_schema_w_attributes().

Referenced by protocols::enzdes::DetectProteinLigandInterfaceOperationCreator::provide_xml_schema().

◆ register_options()

void protocols::enzdes::DetectProteinLigandInterface::register_options ( )

static

References protocols::moves::Mover::register_options().

Referenced by protocols::enzdes::EnzdesBaseProtocol::register_options().

◆ set_design()

void protocols::enzdes::DetectProteinLigandInterface::set_design ( bool const design_in )

inline

References design_.

◆ set_design_target_res()

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

inline

References design_target_res_.

◆ set_detect_interface()

void protocols::enzdes::DetectProteinLigandInterface::set_detect_interface ( bool setting )

inline

References detect_design_interface_.

◆ set_no_design_cys()

void protocols::enzdes::DetectProteinLigandInterface::set_no_design_cys ( bool const no_design_cys_in )

inline

References no_design_cys_.

Member Data Documentation

◆ add_observer_cache_segs_to_interface_

bool protocols::enzdes::DetectProteinLigandInterface::add_observer_cache_segs_to_interface_

private

Referenced by apply(), and parse_tag().

◆ arg_sweep_cutoff_

core::Real protocols::enzdes::DetectProteinLigandInterface::arg_sweep_cutoff_

private

Dicitate the max distance from arginine to ligand for position to be counted as designable.

Referenced by apply(), init_from_options(), and parse_tag().

◆ arg_sweep_interface_

bool protocols::enzdes::DetectProteinLigandInterface::arg_sweep_interface_

private

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

Referenced by apply(), init_from_options(), and parse_tag().

◆ catalytic_res_part_of_interface_

bool protocols::enzdes::DetectProteinLigandInterface::catalytic_res_part_of_interface_

private

interface can be declared as all catalytic res

Referenced by apply(), and parse_tag().

◆ catres_only_

bool protocols::enzdes::DetectProteinLigandInterface::catres_only_

private

Referenced by apply(), and parse_tag().

◆ cstid_list_

std::string protocols::enzdes::DetectProteinLigandInterface::cstid_list_

private

Referenced by apply(), and parse_tag().

◆ cut1_

core::Real protocols::enzdes::DetectProteinLigandInterface::cut1_

private

cut1_ through cut4_ define the shells over which the interface detection takes place

Referenced by apply(), init_from_options(), and parse_tag().

◆ cut2_

core::Real protocols::enzdes::DetectProteinLigandInterface::cut2_

private

Referenced by apply(), init_from_options(), and parse_tag().

◆ cut3_

core::Real protocols::enzdes::DetectProteinLigandInterface::cut3_

private

Referenced by apply(), init_from_options(), and parse_tag().

◆ cut4_

core::Real protocols::enzdes::DetectProteinLigandInterface::cut4_

private

Referenced by apply(), init_from_options(), and parse_tag().

◆ design_

bool protocols::enzdes::DetectProteinLigandInterface::design_

private

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

Referenced by apply(), get_design(), parse_tag(), and set_design().

◆ design_target_res_

std::set< core::Size > protocols::enzdes::DetectProteinLigandInterface::design_target_res_

private

Referenced by apply(), DetectProteinLigandInterface(), and set_design_target_res().

◆ detect_design_interface_

bool protocols::enzdes::DetectProteinLigandInterface::detect_design_interface_

private

Control whether the detect design interface algorithm is run.

Referenced by apply(), get_detect_interface(), init_from_options(), parse_tag(), and set_detect_interface().

◆ no_design_cys_

bool protocols::enzdes::DetectProteinLigandInterface::no_design_cys_

private

Should we prohibit designing to non disulfide cys?

Referenced by apply(), get_no_design_cys(), parse_tag(), and set_no_design_cys().

◆ repack_only_

bool protocols::enzdes::DetectProteinLigandInterface::repack_only_

private

Turn of design (repack_only_), or repacking and design (score_only_)

Referenced by apply(), init_from_options(), and parse_tag().

◆ resfilename_

std::string protocols::enzdes::DetectProteinLigandInterface::resfilename_

private

If resfilename_ is not empty, load it and obey the AUTO directives therein.

Referenced by apply(), init_from_options(), and parse_tag().

◆ score_only_

bool protocols::enzdes::DetectProteinLigandInterface::score_only_

private

Referenced by apply(), init_from_options(), and parse_tag().

◆ use_cstid_list_

bool protocols::enzdes::DetectProteinLigandInterface::use_cstid_list_

private

Referenced by apply(), and parse_tag().

The documentation for this class was generated from the following files:

src/protocols/enzdes/EnzdesTaskOperations.hh
src/protocols/enzdes/EnzdesTaskOperations.cc

Public Types

Public Member Functions

Static Public Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

◆ PackerTask

◆ Pose

◆ TaskOperationOP

Constructor & Destructor Documentation

◆ DetectProteinLigandInterface()

◆ ~DetectProteinLigandInterface()

Member Function Documentation

◆ add_observer_cache_segments_to_set()

◆ apply()

◆ clone()

◆ find_design_interface()

◆ find_design_interface_arg_sweep()

◆ get_design()

◆ get_detect_interface()

◆ get_no_design_cys()

◆ init_from_options()

◆ keyname()

◆ parse_tag()

◆ provide_xml_schema()

◆ register_options()

◆ set_design()

◆ set_design_target_res()

◆ set_detect_interface()

◆ set_no_design_cys()

Member Data Documentation

◆ add_observer_cache_segs_to_interface_

◆ arg_sweep_cutoff_

◆ arg_sweep_interface_

◆ catalytic_res_part_of_interface_

◆ catres_only_

◆ cstid_list_

◆ cut1_

◆ cut2_

◆ cut3_

◆ cut4_

◆ design_

◆ design_target_res_

◆ detect_design_interface_

◆ no_design_cys_

◆ repack_only_

◆ resfilename_

◆ score_only_

◆ use_cstid_list_