#include <LayerDesignOperation.hh>

Inheritance diagram for protocols::flxbb::LayerDesignOperation:

Public Types
enum	LayerOperationType { DESIGN , NO_DESIGN , OMIT }

enum	LayerSpecificationType { DESIGNABLE , PACKABLE , FIXED }

typedef std::string	String

typedef core::Real	Real

typedef core::pose::Pose	Pose

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

typedef core::pack::task::operation::TaskOperation	TaskOperation

typedef core::pack::task::operation::TaskOperationOP	TaskOperationOP

typedef TaskOperation	parent

typedef utility::tag::TagCOP	TagCOP

typedef std::map< std::string, TaskOperationOP >	TaskLayers

typedef std::pair< std::string, TaskOperationOP >	TaskLayer

typedef std::map< std::string, std::string >	LayerDefinitions

typedef std::pair< std::string, std::string >	LayerDefinition

typedef std::map< std::string, LayerDefinitions >	LayerResidues

typedef std::pair< std::string, LayerDefinitions >	Layer

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
	LayerDesignOperation ()
	default constructor More...

	LayerDesignOperation (bool dsgn_core, bool dsgn_boundary, bool dsgn_surface)
	value constructor More...

	LayerDesignOperation (bool dsgn_core, bool dsgn_boundary, bool dsgn_surface, bool Nt, bool Ct, Real core_score, Real surf_score, std::string coreAA, std::string boundaryAA, std::string surfaceAA)
	value constructor More...

	LayerDesignOperation (LayerDesignOperation const &rval)
	Copy constructor. More...

	~LayerDesignOperation () override
	destructor More...

TaskOperationOP	clone () const override
	make clone More...

void	add_layer (std::string const &layer_name, core::pack::task::operation::TaskOperationOP task, LayerOperationType const operation, LayerSpecificationType const specification)
	add a new layer which will be created based on a task operation More...

std::string const &	layer_residues (std::string const &layer_name, std::string const &ss_name) const
	gets the residues allowed for a given secondary structure in a given layer More...

void	set_layer_residues (std::string const &layer_name, std::string const &ss_name, std::string const &residues)
	sets residues allowed for a particular secondary structure in the given layer More...

void	copy_layer_residues (std::string const &src_layer, std::string const &dest_layer)
	copies residues allowed from src to dest More...

void	set_layer_operation (std::string const &layer_name, LayerOperationType const operation)
	sets layer operation More...

void	set_layer_specification (std::string const &layer_name, LayerSpecificationType const specification)
	sets layer specification More...

void	design_layer (bool const dsgn_core, bool const dsgn_boundary, bool const dsgn_surface)
	layer to be designed in internal SRBL object More...

void	sasa_surface (Real const r, String const &ss="")
	accessible surface for evaluating residues are in surface or not More...

void	sasa_core (Real const r, String const &ss="")
	accessible surface for evaluating residues are in core or not More...

void	pore_radius (Real ps)
	set pore radius for colculating asa More...

void	set_verbose (bool const b)
	set verbose More...

void	set_restrict_restypes (bool const b)
	set restrict_restypes More...

void	set_use_sidechain_neighbors (bool const value)
	Set whether to use sidechain neighbors to determine core/boundary/surface (default=false) More...

void	set_sc_neighbor_dist_midpoint (core::Real const &value)
	Set the midpoint of the sigmoidal distance falloff for the sidechain neighbors method. More...

void	set_sc_neighbor_denominator (core::Real const &value)
	Set the factor by which neighbor counts are divided when using the sidechain neighbors method. More...

void	set_sc_neighbor_angle_shift_factor (core::Real const &value)
	Set a parameter in the calculation that the sidechain neighbors algorithm uses. More...

void	set_sc_neighbor_angle_exponent (core::Real const &value)
	Set another parameter (the angle exponent) in the calculation that the sidechain neighbors algorithm uses. More...

void	set_sc_neighbor_dist_exponent (core::Real const &value)
	Set another parameter (the distance exponent) in the calculation that the sidechain neighbors algorithm uses. More...

void	set_design_layers (utility::vector1< std::string > const &layers)
	sets names of layers to design More...

void	use_original_seq ()
	use original sequence for not designed layer More...

void	make_pymol_script (bool value)
	make pymol scripts showing the different layers More...

void	parse_tag (TagCOP tag, DataMap &) override
	Used to parse an xml-like tag to load parameters and properties. More...

void	parse_layer_tag (TagCOP layer_tag, DataMap &datamap)

void	parse_layer_secstruct_tag (TagCOP secstruct_tag, DataMap &datamap, std::string const &layer_name)

void	set_ignore_pikaa_natro (bool const val)
	Sets whether residues set with PIKAA and NATRO in previously-applied resfiles are ignored. More...

bool	ignore_pikaa_natro () const
	Returns whether residues set with PIKAA and NATRO in previously-applied resfiles are ignored. More...

void	apply (Pose const &pose, PackerTask &task) const override
	apply More...

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 Public Attributes
static utility::vector1< std::string > const	SS_TYPES = { "all", "Helix", "HelixCapping", "HelixStart", "Loop", "Strand" }

Private Member Functions
utility::vector1< bool >	get_restrictions (std::string const &layer, std::string const &default_layer, std::string const &ss_type, char const current_aa) const
	gets a list of allowed amino acids, and includes the current amino acid in addition to those allowed by layer More...

utility::vector1< bool >	get_restrictions (std::string const &layer, std::string const &, std::string const &ss_type) const

void	set_default_layer_residues ()

void	set_layer_residues (std::string const &layer_name, std::string const &ss_name, std::string const &residues, LayerResidues &layer_residues)

void	set_use_symmetry (bool const val)
	Set whether this TaskOperation uses a whole, symmetric pose to define layers (true) or just the asymmetric unit (false). Default is true. More...

bool	use_symmetry () const
	Get whether this TaskOperation uses a whole, symmetric pose to define layers (true) or just the asymmetric unit (false). More...

std::string	pos2select (utility::vector1< core::Size > const &pos) const
	utility function to transform a vector of position into a pymol selection command More...

void	write_pymol_script (Pose const &pos, core::select::util::SelectResiduesByLayerOP srbl, std::map< std::string, utility::vector1< bool > > const &layer_specification, bool las_ligand, std::string const &filename) const
	write a pymol command with the different layers as selections More...

Private Attributes
bool	add_helix_capping_
	add helix capping ? More...

bool	use_original_
	use original sequence for not designed layer ? More...

bool	repack_non_designed_residues_

bool	verbose_

bool	restrict_restypes_

bool	make_pymol_script_

LayerResidues	layer_residues_

bool	ignore_pikaa_natro_
	Should residues for which PIKAA or NATRO information was defined in a previously-applied resfile be ignored by LayerDesign? Default is now FALSE. More...

std::map< std::string, bool >	design_layer_

std::map< std::string, LayerSpecificationType >	layer_specification_

std::map< std::string, LayerOperationType >	layer_operation_

TaskLayers	task_layers_

core::select::util::SelectResiduesByLayerOP	srbl_

protocols::parser::BluePrintOP	blueprint_

bool	use_symmetry_
	Should LayerDesign work with symmetry? Default false. More...

Member Typedef Documentation

◆ Layer

typedef std::pair< std::string, LayerDefinitions > protocols::flxbb::LayerDesignOperation::Layer

◆ LayerDefinition

typedef std::pair< std::string, std::string > protocols::flxbb::LayerDesignOperation::LayerDefinition

◆ LayerDefinitions

typedef std::map< std::string, std::string > protocols::flxbb::LayerDesignOperation::LayerDefinitions

◆ LayerResidues

typedef std::map< std::string, LayerDefinitions > protocols::flxbb::LayerDesignOperation::LayerResidues

◆ PackerTask

typedef core::pack::task::PackerTask protocols::flxbb::LayerDesignOperation::PackerTask

◆ parent

typedef TaskOperation protocols::flxbb::LayerDesignOperation::parent

◆ Pose

typedef core::pose::Pose protocols::flxbb::LayerDesignOperation::Pose

◆ Real

typedef core::Real protocols::flxbb::LayerDesignOperation::Real

◆ String

typedef std::string protocols::flxbb::LayerDesignOperation::String

◆ TagCOP

typedef utility::tag::TagCOP protocols::flxbb::LayerDesignOperation::TagCOP

◆ TaskLayer

typedef std::pair< std::string, TaskOperationOP > protocols::flxbb::LayerDesignOperation::TaskLayer

◆ TaskLayers

typedef std::map< std::string, TaskOperationOP > protocols::flxbb::LayerDesignOperation::TaskLayers

◆ TaskOperation

typedef core::pack::task::operation::TaskOperation protocols::flxbb::LayerDesignOperation::TaskOperation

◆ TaskOperationOP

typedef core::pack::task::operation::TaskOperationOP protocols::flxbb::LayerDesignOperation::TaskOperationOP

Member Enumeration Documentation

◆ LayerOperationType

enum protocols::flxbb::LayerDesignOperation::LayerOperationType

Enumerator
DESIGN
NO_DESIGN
OMIT

◆ LayerSpecificationType

enum protocols::flxbb::LayerDesignOperation::LayerSpecificationType

Enumerator
DESIGNABLE
PACKABLE
FIXED

Constructor & Destructor Documentation

◆ LayerDesignOperation() [1/4]

protocols::flxbb::LayerDesignOperation::LayerDesignOperation ( )

default constructor

References set_default_layer_residues().

◆ LayerDesignOperation() [2/4]

protocols::flxbb::LayerDesignOperation::LayerDesignOperation	(	bool	dsgn_core,
		bool	dsgn_boundary,
		bool	dsgn_surface
	)

value constructor

References design_layer(), and set_default_layer_residues().

◆ LayerDesignOperation() [3/4]

protocols::flxbb::LayerDesignOperation::LayerDesignOperation	(	bool	dsgn_core,
		bool	dsgn_boundary,
		bool	dsgn_surface,
		bool	Nt,
		bool	Ct,
		Real	core_score,
		Real	surf_score,
		std::string	coreAA,
		std::string	boundaryAA,
		std::string	surfaceAA
	)

value constructor

References design_layer(), design_layer_, layer_residues_, set_default_layer_residues(), and srbl_.

◆ LayerDesignOperation() [4/4]

protocols::flxbb::LayerDesignOperation::LayerDesignOperation ( LayerDesignOperation const & rval )

default

Copy constructor.

◆ ~LayerDesignOperation()

protocols::flxbb::LayerDesignOperation::~LayerDesignOperation ( )

overridedefault

destructor

Member Function Documentation

◆ add_layer()

void protocols::flxbb::LayerDesignOperation::add_layer	(	std::string const &	layer_name,
		core::pack::task::operation::TaskOperationOP	task,
		LayerOperationType const	operation,
		LayerSpecificationType const	specification
	)

add a new layer which will be created based on a task operation

layer to be designed

References design_layer_, layer_operation_, layer_residues_, layer_specification_, and task_layers_.

Referenced by parse_layer_tag().

◆ apply()

void protocols::flxbb::LayerDesignOperation::apply	(	Pose const &	pose,
		PackerTask &	task
	)		const

overridevirtual

apply

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

References add_helix_capping_, blueprint_, core::pack::task::ResidueLevelTask::command_string(), design_layer_, DESIGNABLE, protocols::simple_filters::dssp(), core::pose::symmetry::extract_asymmetric_unit(), core::chemical::element::F, protocols::flxbb::find_ligands(), FIXED, get_restrictions(), ignore_pikaa_natro(), core::conformation::Residue::is_lower_terminus(), core::conformation::Residue::is_protein(), core::pose::symmetry::is_symmetric(), core::conformation::Residue::is_upper_terminus(), layer_operation_, layer_specification_, make_pymol_script_, NO_DESIGN, core::pack::task::PackerTask::nonconst_residue_task(), OMIT, PACKABLE, core::pack::task::ResidueLevelTask::prevent_repacking(), repack_non_designed_residues_, protocols::forge::methods::replace(), core::pose::Pose::residue(), core::pack::task::PackerTask::residue_task(), core::pack::task::ResidueLevelTask::restrict_absent_canonical_aas(), core::pack::task::ResidueLevelTask::restrict_to_repacking(), core::pose::Pose::size(), srbl_, task_layers_, protocols::TR(), use_symmetry(), verbose_, and write_pymol_script().

◆ clone()

core::pack::task::operation::TaskOperationOP protocols::flxbb::LayerDesignOperation::clone ( ) const

overridevirtual

make clone

clone

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

◆ copy_layer_residues()

void protocols::flxbb::LayerDesignOperation::copy_layer_residues	(	std::string const &	src_layer,
		std::string const &	dest_layer
	)

copies residues allowed from src to dest

References layer_residues_.

Referenced by parse_layer_secstruct_tag().

◆ design_layer()

void protocols::flxbb::LayerDesignOperation::design_layer	(	bool const	dsgn_core,
		bool const	dsgn_boundary,
		bool const	dsgn_surface
	)

layer to be designed in internal SRBL object

layer to be designed

References srbl_.

Referenced by LayerDesignOperation().

◆ get_restrictions() [1/2]

utility::vector1< bool > protocols::flxbb::LayerDesignOperation::get_restrictions	(	std::string const &	layer,
		std::string const &	,
		std::string const &	ss_type
	)		const

private

References core::chemical::aa_from_oneletter_code(), layer_residues_, and core::chemical::num_canonical_aas.

◆ get_restrictions() [2/2]

utility::vector1< bool > protocols::flxbb::LayerDesignOperation::get_restrictions	(	std::string const &	layer,
		std::string const &	default_layer,
		std::string const &	ss_type,
		char const	current_aa
	)		const

private

gets a list of allowed amino acids, and includes the current amino acid in addition to those allowed by layer

Referenced by apply().

◆ ignore_pikaa_natro()

bool protocols::flxbb::LayerDesignOperation::ignore_pikaa_natro ( ) const

inline

Returns whether residues set with PIKAA and NATRO in previously-applied resfiles are ignored.

Default behaviour is now FALSE to preserve commutativity.

References ignore_pikaa_natro_.

Referenced by apply().

◆ keyname()

static std::string protocols::flxbb::LayerDesignOperation::keyname ( )

inlinestatic

Referenced by provide_xml_schema().

◆ layer_residues()

std::string const & protocols::flxbb::LayerDesignOperation::layer_residues	(	std::string const &	layer_name,
		std::string const &	ss_name
	)		const

gets the residues allowed for a given secondary structure in a given layer

References layer_residues_.

Referenced by set_layer_residues().

◆ make_pymol_script()

void protocols::flxbb::LayerDesignOperation::make_pymol_script ( bool value )

inline

make pymol scripts showing the different layers

References make_pymol_script_.

Referenced by parse_tag().

◆ parse_layer_secstruct_tag()

void protocols::flxbb::LayerDesignOperation::parse_layer_secstruct_tag	(	TagCOP	secstruct_tag,
		DataMap &	datamap,
		std::string const &	layer_name
	)

References protocols::cluster::calibur::aa, copy_layer_residues(), DESIGN, DESIGNABLE, core::sequence::end, FIXED, layer_residues_, NO_DESIGN, OMIT, PACKABLE, set_layer_operation(), set_layer_residues(), set_layer_specification(), protocols::TR(), and protocols::flxbb::unique_chars().

Referenced by parse_layer_tag().

◆ parse_layer_tag()

void protocols::flxbb::LayerDesignOperation::parse_layer_tag	(	TagCOP	layer_tag,
		DataMap &	datamap
	)

References add_layer(), DESIGN, DESIGNABLE, layer_residues_, parse_layer_secstruct_tag(), set_layer_residues(), SS_TYPES, and protocols::TR().

Referenced by parse_tag().

◆ parse_tag()

void protocols::flxbb::LayerDesignOperation::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 blueprint_, design_layer_, layer_residues_, core::scoring::sasa::LJ, make_pymol_script(), parse_layer_tag(), repack_non_designed_residues_, set_design_layers(), set_ignore_pikaa_natro(), set_restrict_restypes(), set_sc_neighbor_angle_exponent(), set_sc_neighbor_angle_shift_factor(), set_sc_neighbor_denominator(), set_sc_neighbor_dist_exponent(), set_sc_neighbor_dist_midpoint(), set_use_sidechain_neighbors(), set_use_symmetry(), set_verbose(), srbl_, protocols::TR(), and use_original_.

◆ pore_radius()

void protocols::flxbb::LayerDesignOperation::pore_radius ( Real ps )

set pore radius for colculating asa

References srbl_.

◆ pos2select()

std::string protocols::flxbb::LayerDesignOperation::pos2select ( utility::vector1< core::Size > const & pos ) const

private

utility function to transform a vector of position into a pymol selection command

References protocols::kinmatch::str(), and core::id::to_string().

Referenced by write_pymol_script().

◆ provide_xml_schema()

void protocols::flxbb::LayerDesignOperation::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References core::pack::task::operation::complex_type_name_for_task_op(), keyname(), protocols::flxbb::layer_design_ss_layer_group(), protocols::flxbb::layer_design_ss_layer_naming_func(), protocols::flxbb::layer_design_ss_layer_or_taskop_group(), and SS_TYPES.

◆ sasa_core()

void protocols::flxbb::LayerDesignOperation::sasa_core	(	Real const	r,
		String const &	ss = `""`
	)

accessible surface for evaluating residues are in core or not

References srbl_.

◆ sasa_surface()

void protocols::flxbb::LayerDesignOperation::sasa_surface	(	Real const	r,
		String const &	ss = `""`
	)

accessible surface for evaluating residues are in surface or not

References srbl_.

◆ set_default_layer_residues()

void protocols::flxbb::LayerDesignOperation::set_default_layer_residues ( )

private

References DESIGN, design_layer_, DESIGNABLE, layer_operation_, layer_residues_, layer_specification_, and protocols::TR().

Referenced by LayerDesignOperation().

◆ set_design_layers()

void protocols::flxbb::LayerDesignOperation::set_design_layers ( utility::vector1< std::string > const & layers )

sets names of layers to design

References design_layer_.

Referenced by parse_tag().

◆ set_ignore_pikaa_natro()

void protocols::flxbb::LayerDesignOperation::set_ignore_pikaa_natro ( bool const val )

inline

Sets whether residues set with PIKAA and NATRO in previously-applied resfiles are ignored.

Default behaviour is now FALSE to preserve commutativity.

References ignore_pikaa_natro_, and protocols::hybridization::val.

Referenced by parse_tag().

◆ set_layer_operation()

void protocols::flxbb::LayerDesignOperation::set_layer_operation	(	std::string const &	layer_name,
		LayerOperationType const	operation
	)

sets layer operation

References layer_operation_.

Referenced by parse_layer_secstruct_tag().

◆ set_layer_residues() [1/2]

void protocols::flxbb::LayerDesignOperation::set_layer_residues	(	std::string const &	layer_name,
		std::string const &	ss_name,
		std::string const &	residues
	)

sets residues allowed for a particular secondary structure in the given layer

References layer_residues_.

Referenced by parse_layer_secstruct_tag(), and parse_layer_tag().

◆ set_layer_residues() [2/2]

void protocols::flxbb::LayerDesignOperation::set_layer_residues	(	std::string const &	layer_name,
		std::string const &	ss_name,
		std::string const &	residues,
		LayerResidues &	layer_residues
	)

private

References layer_residues(), and layer_residues_.

◆ set_layer_specification()

void protocols::flxbb::LayerDesignOperation::set_layer_specification	(	std::string const &	layer_name,
		LayerSpecificationType const	specification
	)

sets layer specification

References layer_specification_.

Referenced by parse_layer_secstruct_tag().

◆ set_restrict_restypes()

void protocols::flxbb::LayerDesignOperation::set_restrict_restypes ( bool const b )

inline

set restrict_restypes

References protocols::match::upstream::b, and restrict_restypes_.

Referenced by parse_tag().

◆ set_sc_neighbor_angle_exponent()

void protocols::flxbb::LayerDesignOperation::set_sc_neighbor_angle_exponent ( core::Real const & value )

Set another parameter (the angle exponent) in the calculation that the sidechain neighbors algorithm uses.

See core::select::util::SelectResiduesByLayer class for details.

References srbl_.

Referenced by parse_tag().

◆ set_sc_neighbor_angle_shift_factor()

void protocols::flxbb::LayerDesignOperation::set_sc_neighbor_angle_shift_factor ( core::Real const & value )

Set a parameter in the calculation that the sidechain neighbors algorithm uses.

See core::select::util::SelectResiduesByLayer class for details.

References srbl_.

Referenced by parse_tag().

◆ set_sc_neighbor_denominator()

void protocols::flxbb::LayerDesignOperation::set_sc_neighbor_denominator ( core::Real const & value )

Set the factor by which neighbor counts are divided when using the sidechain neighbors method.

References srbl_.

Referenced by parse_tag().

◆ set_sc_neighbor_dist_exponent()

void protocols::flxbb::LayerDesignOperation::set_sc_neighbor_dist_exponent ( core::Real const & value )

Set another parameter (the distance exponent) in the calculation that the sidechain neighbors algorithm uses.

See core::select::util::SelectResiduesByLayer class for details.

References srbl_.

Referenced by parse_tag().

◆ set_sc_neighbor_dist_midpoint()

void protocols::flxbb::LayerDesignOperation::set_sc_neighbor_dist_midpoint ( core::Real const & value )

Set the midpoint of the sigmoidal distance falloff for the sidechain neighbors method.

References srbl_.

Referenced by parse_tag().

◆ set_use_sidechain_neighbors()

void protocols::flxbb::LayerDesignOperation::set_use_sidechain_neighbors ( bool const value )

Set whether to use sidechain neighbors to determine core/boundary/surface (default=false)

References srbl_.

Referenced by parse_tag().

◆ set_use_symmetry()

void protocols::flxbb::LayerDesignOperation::set_use_symmetry ( bool const val )

inlineprivate

Set whether this TaskOperation uses a whole, symmetric pose to define layers (true) or just the asymmetric unit (false). Default is true.

References use_symmetry_, and protocols::hybridization::val.

Referenced by parse_tag().

◆ set_verbose()

void protocols::flxbb::LayerDesignOperation::set_verbose ( bool const b )

inline

set verbose

References protocols::match::upstream::b, and verbose_.

Referenced by parse_tag().

◆ use_original_seq()

void protocols::flxbb::LayerDesignOperation::use_original_seq ( )

inline

use original sequence for not designed layer

References use_original_.

◆ use_symmetry()

bool protocols::flxbb::LayerDesignOperation::use_symmetry ( ) const

inlineprivate

Get whether this TaskOperation uses a whole, symmetric pose to define layers (true) or just the asymmetric unit (false).

References use_symmetry_.

Referenced by apply().

◆ write_pymol_script()

void protocols::flxbb::LayerDesignOperation::write_pymol_script	(	Pose const &	pos,
		core::select::util::SelectResiduesByLayerOP	srbl,
		std::map< std::string, utility::vector1< bool > > const &	layer_specification,
		bool	las_ligand,
		std::string const &	filename
	)		const

private

write a pymol command with the different layers as selections

References core::pose::Pose::dump_pdb(), protocols::abinitio::filename(), pos2select(), core::pose::Pose::size(), and protocols::TR().

Referenced by apply().

Member Data Documentation

◆ add_helix_capping_

bool protocols::flxbb::LayerDesignOperation::add_helix_capping_

private

add helix capping ?

Referenced by apply().

◆ blueprint_

protocols::parser::BluePrintOP protocols::flxbb::LayerDesignOperation::blueprint_

private

Referenced by apply(), and parse_tag().

◆ design_layer_

std::map< std::string, bool > protocols::flxbb::LayerDesignOperation::design_layer_

private

Referenced by add_layer(), apply(), LayerDesignOperation(), parse_tag(), set_default_layer_residues(), and set_design_layers().

◆ ignore_pikaa_natro_

bool protocols::flxbb::LayerDesignOperation::ignore_pikaa_natro_

private

Should residues for which PIKAA or NATRO information was defined in a previously-applied resfile be ignored by LayerDesign? Default is now FALSE.

Author: Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

Referenced by ignore_pikaa_natro(), and set_ignore_pikaa_natro().

◆ layer_operation_

std::map< std::string, LayerOperationType > protocols::flxbb::LayerDesignOperation::layer_operation_

private

Referenced by add_layer(), apply(), set_default_layer_residues(), and set_layer_operation().

◆ layer_residues_

LayerResidues protocols::flxbb::LayerDesignOperation::layer_residues_

private

Referenced by add_layer(), copy_layer_residues(), get_restrictions(), layer_residues(), LayerDesignOperation(), parse_layer_secstruct_tag(), parse_layer_tag(), parse_tag(), set_default_layer_residues(), and set_layer_residues().

◆ layer_specification_

std::map< std::string, LayerSpecificationType > protocols::flxbb::LayerDesignOperation::layer_specification_

private

Referenced by add_layer(), apply(), set_default_layer_residues(), and set_layer_specification().

◆ make_pymol_script_

bool protocols::flxbb::LayerDesignOperation::make_pymol_script_

private

Referenced by apply(), and make_pymol_script().

◆ repack_non_designed_residues_

bool protocols::flxbb::LayerDesignOperation::repack_non_designed_residues_

private

Referenced by apply(), and parse_tag().

◆ restrict_restypes_

bool protocols::flxbb::LayerDesignOperation::restrict_restypes_

private

Referenced by set_restrict_restypes().

◆ srbl_

core::select::util::SelectResiduesByLayerOP protocols::flxbb::LayerDesignOperation::srbl_

private

Referenced by apply(), design_layer(), LayerDesignOperation(), parse_tag(), pore_radius(), sasa_core(), sasa_surface(), set_sc_neighbor_angle_exponent(), set_sc_neighbor_angle_shift_factor(), set_sc_neighbor_denominator(), set_sc_neighbor_dist_exponent(), set_sc_neighbor_dist_midpoint(), and set_use_sidechain_neighbors().

◆ SS_TYPES

utility::vector1< std::string > const protocols::flxbb::LayerDesignOperation::SS_TYPES = { "all", "Helix", "HelixCapping", "HelixStart", "Loop", "Strand" }

static

Referenced by parse_layer_tag(), and provide_xml_schema().

◆ task_layers_

TaskLayers protocols::flxbb::LayerDesignOperation::task_layers_

private

Referenced by add_layer(), and apply().

◆ use_original_

bool protocols::flxbb::LayerDesignOperation::use_original_

private

use original sequence for not designed layer ?

Referenced by parse_tag(), and use_original_seq().

◆ use_symmetry_

bool protocols::flxbb::LayerDesignOperation::use_symmetry_

private

Should LayerDesign work with symmetry? Default false.

If false, the asymmetric unit is extracted and used for layer setup. If true (default), the whole, symmetric pose is used for layer setup.

Referenced by set_use_symmetry(), and use_symmetry().

◆ verbose_

bool protocols::flxbb::LayerDesignOperation::verbose_

private

Referenced by apply(), and set_verbose().

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

src/protocols/flxbb/LayerDesignOperation.hh
src/protocols/flxbb/LayerDesignOperation.cc

Public Types

Public Member Functions

Static Public Member Functions

Static Public Attributes

Private Member Functions

Private Attributes

Member Typedef Documentation

◆ Layer

◆ LayerDefinition

◆ LayerDefinitions

◆ LayerResidues

◆ PackerTask

◆ parent

◆ Pose

◆ Real

◆ String

◆ TagCOP

◆ TaskLayer

◆ TaskLayers

◆ TaskOperation

◆ TaskOperationOP

Member Enumeration Documentation

◆ LayerOperationType

◆ LayerSpecificationType

Constructor & Destructor Documentation

◆ LayerDesignOperation() [1/4]

◆ LayerDesignOperation() [2/4]

◆ LayerDesignOperation() [3/4]

◆ LayerDesignOperation() [4/4]

◆ ~LayerDesignOperation()

Member Function Documentation

◆ add_layer()

◆ apply()

◆ clone()

◆ copy_layer_residues()

◆ design_layer()

◆ get_restrictions() [1/2]

◆ get_restrictions() [2/2]

◆ ignore_pikaa_natro()

◆ keyname()

◆ layer_residues()

◆ make_pymol_script()

◆ parse_layer_secstruct_tag()

◆ parse_layer_tag()

◆ parse_tag()

◆ pore_radius()

◆ pos2select()

◆ provide_xml_schema()

◆ sasa_core()

◆ sasa_surface()

◆ set_default_layer_residues()

◆ set_design_layers()

◆ set_ignore_pikaa_natro()

◆ set_layer_operation()

◆ set_layer_residues() [1/2]

◆ set_layer_residues() [2/2]

◆ set_layer_specification()

◆ set_restrict_restypes()

◆ set_sc_neighbor_angle_exponent()

◆ set_sc_neighbor_angle_shift_factor()

◆ set_sc_neighbor_denominator()

◆ set_sc_neighbor_dist_exponent()

◆ set_sc_neighbor_dist_midpoint()

◆ set_use_sidechain_neighbors()

◆ set_use_symmetry()

◆ set_verbose()

◆ use_original_seq()

◆ use_symmetry()

◆ write_pymol_script()

Member Data Documentation

◆ add_helix_capping_

◆ blueprint_

◆ design_layer_

◆ ignore_pikaa_natro_

◆ layer_operation_

◆ layer_residues_

◆ layer_specification_

◆ make_pymol_script_

◆ repack_non_designed_residues_

◆ restrict_restypes_