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protocols::enzdes::DetectProteinLigandInterface Class Reference

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:
Inheritance graph
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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::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 bool task_operation_provides_citation_info () const
 Does this task operation provide information about how to cite it? More...
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. More...
 
virtual bool task_operation_is_unpublished () const
 Does this task_operation indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. 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::Sizedesign_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

Constructor & Destructor Documentation

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

Member Function Documentation

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

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.

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

References design_.

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

References no_design_cys_.

void protocols::enzdes::DetectProteinLigandInterface::init_from_options ( )
static std::string protocols::enzdes::DetectProteinLigandInterface::keyname ( )
inlinestatic
void protocols::enzdes::DetectProteinLigandInterface::parse_tag ( TagCOP  tag,
DataMap  
)
overridevirtual
void protocols::enzdes::DetectProteinLigandInterface::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::enzdes::DetectProteinLigandInterface::register_options ( )
static
void protocols::enzdes::DetectProteinLigandInterface::set_design ( bool const  design_in)
inline

References design_.

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

References design_target_res_.

void protocols::enzdes::DetectProteinLigandInterface::set_detect_interface ( bool  setting)
inline
void protocols::enzdes::DetectProteinLigandInterface::set_no_design_cys ( bool const  no_design_cys_in)
inline

References no_design_cys_.

Member Data Documentation

bool protocols::enzdes::DetectProteinLigandInterface::add_observer_cache_segs_to_interface_
private

Referenced by apply(), and parse_tag().

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().

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().

bool protocols::enzdes::DetectProteinLigandInterface::catalytic_res_part_of_interface_
private

interface can be declared as all catalytic res

Referenced by apply(), and parse_tag().

bool protocols::enzdes::DetectProteinLigandInterface::catres_only_
private

Referenced by apply(), and parse_tag().

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

Referenced by apply(), and parse_tag().

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().

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

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

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

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

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

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

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().

std::set< core::Size > protocols::enzdes::DetectProteinLigandInterface::design_target_res_
private
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().

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().

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().

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().

bool protocols::enzdes::DetectProteinLigandInterface::score_only_
private

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

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: