protocols::flxbb::LayerDesignOperation Class Reference

#include <LayerDesignOperation.hh>

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 Member Functions
	LayerDesignOperation ()
	default constructor More...
	LayerDesignOperation (bool dsgn_core, bool dsgn_boundary, bool dsgn_surface)
	value constructor More...
	LayerDesignOperation (LayerDesignOperation const &rval)
virtual	~LayerDesignOperation ()
	destructor More...
virtual TaskOperationOP	clone () const
	make clone More...
void	design_layer (bool const dsgn_core, bool const dsgn_boundary, bool const dsgn_surface)
	layer to be designed 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	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 &)
virtual void	apply (Pose const &pose, PackerTask &task) const
	apply More...

Private Member Functions
utility::vector1< bool >	get_restrictions (std::string const &layer, std::string const &default_layer, std::string const &ss_type) const
void	set_default_layer_residues ()
std::string	pos2select (utility::vector1< 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, toolbox::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_
std::map< std::string, bool >	design_layer_
std::map< std::string, LayerSpecificationType >	layer_specification_
std::map< std::string, LayerOperationType >	layer_operation_
TaskLayers	task_layers_
toolbox::SelectResiduesByLayerOP	srbl_
protocols::jd2::parser::BluePrintOP	blueprint_

Member Typedef Documentation

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Member Enumeration Documentation

enum protocols::flxbb::LayerDesignOperation::LayerOperationType

Enumerator
DESIGN
NO_DESIGN
OMIT

enum protocols::flxbb::LayerDesignOperation::LayerSpecificationType

Enumerator
DESIGNABLE
PACKABLE
FIXED

Constructor & Destructor Documentation

protocols::flxbb::LayerDesignOperation::LayerDesignOperation

(

)

default constructor

References set_default_layer_residues().

Referenced by clone().

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

value constructor

References design_layer(), and set_default_layer_residues().

protocols::flxbb::LayerDesignOperation::LayerDesignOperation

(

LayerDesignOperation const &

rval

)

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

virtual

destructor

Member Function Documentation

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

virtual

apply

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

References add_helix_capping_, blueprint_, core::pack::task::ResidueLevelTask::command_string(), design, design_layer_, DESIGNABLE, core::pack::task::PackerTask_::designing_residues(), protocols::simple_filters::dssp(), core::scoring::dssp::Dssp::dssp_reduced(), core::pose::symmetry::extract_asymmetric_unit(), utility::file::file_exists(), protocols::flxbb::find_ligands(), fixed, FIXED, core::scoring::dssp::Dssp::get_dssp_secstruct(), get_restrictions(), core::conformation::Residue::is_lower_terminus(), core::conformation::Residue::is_protein(), core::pose::symmetry::is_symmetric(), core::conformation::Residue::is_upper_terminus(), layer, 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_, core::pack::task::PackerTask_::repacking_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(), runtime_assert, s, secstruct, srbl_, ss, task_layers_, core::pose::Pose::total_residue(), protocols::TR, type, verbose_, and write_pymol_script().

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

virtual

make clone

clone

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

References LayerDesignOperation().

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

layer to be designed

References srbl_.

Referenced by LayerDesignOperation().

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

private

References layer_residues_, and restype.

Referenced by apply().

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

inline

make pymol scripts showing the different layers

Referenced by parse_tag().

void protocols::flxbb::LayerDesignOperation::parse_tag	(	TagCOP	tag,
		DataMap &	datamap
	)

References blueprint_, DESIGN, design_layer_, DESIGNABLE, FIXED, layer, layer_operation_, layer_residues_, layer_specification_, make_pymol_script(), NO_DESIGN, OMIT, PACKABLE, repack_non_designed_residues_, secstruct, set_restrict_restypes(), set_verbose(), srbl_, utility::string_split(), task_layers_, protocols::TR, use_original_, and utility_exit_with_message.

void protocols::flxbb::LayerDesignOperation::pore_radius

(

Real

ps

)

set pore radius for colculating asa

References srbl_.

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

private

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

References protocols::kinmatch::str().

Referenced by write_pymol_script().

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

accessible surface for evaluating residues are in core or not

References srbl_.

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

accessible surface for evaluating residues are in surface or not

References srbl_.

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

private

References DESIGN, design_layer_, DESIGNABLE, protocols::cyclic_peptide::insert, layer_operation_, layer_residues_, layer_specification_, protocols::flxbb::makeMap(), and protocols::TR.

Referenced by LayerDesignOperation().

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

inline

set restrict_restypes

References protocols::match::upstream::b.

Referenced by parse_tag().

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

inline

set verbose

References protocols::match::upstream::b.

Referenced by parse_tag().

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

inline

use original sequence for not designed layer

void protocols::flxbb::LayerDesignOperation::write_pymol_script ( Pose const &  pos, toolbox::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(), layer, pos2select(), core::pose::Pose::total_residue(), and protocols::TR.

Referenced by apply().

Member Data Documentation

bool protocols::flxbb::LayerDesignOperation::add_helix_capping_

private

add helix capping ?

Referenced by apply().

protocols::jd2::parser::BluePrintOP protocols::flxbb::LayerDesignOperation::blueprint_

private

Referenced by apply(), and parse_tag().

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

private

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

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

private

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

LayerResidues protocols::flxbb::LayerDesignOperation::layer_residues_

private

Referenced by get_restrictions(), parse_tag(), and set_default_layer_residues().

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

private

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

bool protocols::flxbb::LayerDesignOperation::make_pymol_script_

private

Referenced by apply().

bool protocols::flxbb::LayerDesignOperation::repack_non_designed_residues_

private

Referenced by apply(), and parse_tag().

bool protocols::flxbb::LayerDesignOperation::restrict_restypes_

private

toolbox::SelectResiduesByLayerOP protocols::flxbb::LayerDesignOperation::srbl_

private

Referenced by apply(), design_layer(), parse_tag(), pore_radius(), sasa_core(), and sasa_surface().

TaskLayers protocols::flxbb::LayerDesignOperation::task_layers_

private

Referenced by apply(), and parse_tag().

bool protocols::flxbb::LayerDesignOperation::use_original_

private

use original sequence for not designed layer ?

Referenced by parse_tag().

bool protocols::flxbb::LayerDesignOperation::verbose_

private

Referenced by apply().

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

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