protocols::dna::RestrictDesignToProteinDNAInterface Class Reference

#include <RestrictDesignToProteinDNAInterface.hh>

Inheritance diagram for protocols::dna::RestrictDesignToProteinDNAInterface:

Public Types
typedef core::pose::Pose	Pose
typedef core::pose::PoseCOP	PoseCOP
typedef core::pack::task::operation::TaskOperation	TaskOperation
typedef core::pack::task::operation::TaskOperationOP	TaskOperationOP
typedef core::pack::task::PackerTask	PackerTask
typedef TaskOperation	parent
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
	RestrictDesignToProteinDNAInterface ()
	~RestrictDesignToProteinDNAInterface () override
TaskOperationOP	clone () const override
	Create another task operation of the type matching the most-derived version of the class. More...
void	apply (Pose const &pose, PackerTask &ptask) const override
	determines the DNA interface residues and informs a PackerTask of their appropriate packing behavior More...
void	copy_dna_chains (DnaChainsCOP chains)
DnaChainsCOP	dna_chains () const
void	copy_targeted_dna (DnaDesignDefOPs const &targeted_dna)
DnaDesignDefOPs const &	targeted_dna () const
void	copy_interface (DnaInterfaceFinderCOP interface)
DnaInterfaceFinderCOP	interface () const
void	set_reference_pose (PoseCOP pose)
PoseCOP	reference_pose () const
void	set_base_only (bool value)
bool	base_only () const
void	set_forget_chains_and_interface (bool value)
bool	forget_chains_and_interface () const
void	parse_tag (TagCOP, DataMap &) override
	Used to parse an xml-like tag to load parameters and properties. 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 ()

Private Attributes
DnaChainsOP	dna_chains_
DnaDesignDefOPs	targeted_dna_
DnaInterfaceFinderOP	interface_
PoseCOP	reference_pose_
bool	base_only_
bool	forget_chains_and_interface_
core::Real	z_cutoff_
core::Real	close_threshold_
core::Real	contact_threshold_

Member Typedef Documentation

PackerTask

typedef core::pack::task::PackerTask protocols::dna::RestrictDesignToProteinDNAInterface::PackerTask

parent

typedef TaskOperation protocols::dna::RestrictDesignToProteinDNAInterface::parent

Pose

typedef core::pose::Pose protocols::dna::RestrictDesignToProteinDNAInterface::Pose

PoseCOP

typedef core::pose::PoseCOP protocols::dna::RestrictDesignToProteinDNAInterface::PoseCOP

TaskOperation

typedef core::pack::task::operation::TaskOperation protocols::dna::RestrictDesignToProteinDNAInterface::TaskOperation

TaskOperationOP

typedef core::pack::task::operation::TaskOperationOP protocols::dna::RestrictDesignToProteinDNAInterface::TaskOperationOP

Constructor & Destructor Documentation

RestrictDesignToProteinDNAInterface()

protocols::dna::RestrictDesignToProteinDNAInterface::RestrictDesignToProteinDNAInterface

(

)

~RestrictDesignToProteinDNAInterface()

protocols::dna::RestrictDesignToProteinDNAInterface::~RestrictDesignToProteinDNAInterface ( )

overridedefault

Member Function Documentation

apply()

void protocols::dna::RestrictDesignToProteinDNAInterface::apply ( Pose const &  pose, PackerTask &  ptask  ) const

overridevirtual

determines the DNA interface residues and informs a PackerTask of their appropriate packing behavior

Step 2: get info about DNA chains and set up DNA packing behavior Step 3: Determine protein-DNA interface Step 4: apply any new restrictions to resfile pack/design settings, and any existing constraints Step 5: report

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

References core::chemical::ResidueTypeBase::aa(), core::pack::task::ResidueLevelTask::add_behavior(), core::pack::task::ResidueLevelTask::allowed_residue_types_begin(), core::pack::task::ResidueLevelTask::allowed_residue_types_end(), base_only_, core::pack::task::ResidueLevelTask::being_designed(), core::pack::task::ResidueLevelTask::being_packed(), protocols::dna::DnaPosition::bottom(), core::pose::Pose::chain(), protocols::dna::DnaNeighbor::close(), close_threshold_, core::pose::Pose::constraint_set(), protocols::dna::DnaNeighbor::contact(), contact_threshold_, dna_chains_, protocols::dna::dna_comp_name_str(), core::sequence::end, core::pose::PDBPoseMap::find(), protocols::dna::find_basepairs(), forget_chains_and_interface_, core::chemical::ResidueTypeFinder::get_all_possible_residue_types(), core::pack::task::ResidueLevelTask::has_behavior(), interface_, core::chemical::ResidueTypeBase::is_DNA(), core::chemical::ResidueTypeBase::is_protein(), core::conformation::Residue::name3(), core::chemical::ResidueTypeFinder::name3(), core::pack::task::PackerTask::nonconst_residue_task(), core::chemical::num_canonical_aas, core::pack::task::PackerTask::pack_residue(), protocols::dna::DnaPosition::paired(), core::pose::Pose::pdb_info(), core::pack::task::ResidueLevelTask::prevent_repacking(), core::pack::task::ResidueLevelTask::print_allowed_types(), reference_pose_, core::pose::Pose::residue(), core::pack::task::PackerTask::residue_task(), core::pose::Pose::residue_type(), core::pose::Pose::residue_type_set_for_pose(), core::pack::task::ResidueLevelTask::restrict_absent_canonical_aas(), core::pose::Pose::size(), core::pack::task::ResidueLevelTask::target_type(), targeted_dna_, protocols::dna::DnaPosition::top(), core::pack::task::PackerTask::total_residue(), protocols::dna::TR(), and z_cutoff_.

base_only()

bool protocols::dna::RestrictDesignToProteinDNAInterface::base_only ( ) const

inline

References base_only_.

clone()

TaskOperationOP protocols::dna::RestrictDesignToProteinDNAInterface::clone ( ) const

overridevirtual

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

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

copy_dna_chains()

void protocols::dna::RestrictDesignToProteinDNAInterface::copy_dna_chains

(

DnaChainsCOP

chains

)

References dna_chains(), and dna_chains_.

copy_interface()

void protocols::dna::RestrictDesignToProteinDNAInterface::copy_interface

(

DnaInterfaceFinderCOP

interface

)

References interface(), and interface_.

copy_targeted_dna()

void protocols::dna::RestrictDesignToProteinDNAInterface::copy_targeted_dna

(

DnaDesignDefOPs const &

targeted_dna

)

References targeted_dna(), and targeted_dna_.

dna_chains()

DnaChainsCOP protocols::dna::RestrictDesignToProteinDNAInterface::dna_chains

(

)

const

References dna_chains_.

Referenced by copy_dna_chains().

forget_chains_and_interface()

bool protocols::dna::RestrictDesignToProteinDNAInterface::forget_chains_and_interface ( ) const

inline

References forget_chains_and_interface_.

interface()

DnaInterfaceFinderCOP protocols::dna::RestrictDesignToProteinDNAInterface::interface

(

)

const

References interface_.

Referenced by copy_interface().

keyname()

static std::string protocols::dna::RestrictDesignToProteinDNAInterface::keyname ( )

inlinestatic

Referenced by provide_xml_schema().

parse_tag()

void protocols::dna::RestrictDesignToProteinDNAInterface::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 base_only_, close_threshold_, forget_chains_and_interface_, protocols::dna::load_dna_design_defs_from_options(), protocols::dna::load_dna_design_defs_from_strings(), targeted_dna_, protocols::dna::TR(), and z_cutoff_.

provide_xml_schema()

void protocols::dna::RestrictDesignToProteinDNAInterface::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd )

static

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

reference_pose()

PoseCOP protocols::dna::RestrictDesignToProteinDNAInterface::reference_pose

(

)

const

References reference_pose_.

set_base_only()

void protocols::dna::RestrictDesignToProteinDNAInterface::set_base_only ( bool  value )

inline

References base_only_.

set_forget_chains_and_interface()

void protocols::dna::RestrictDesignToProteinDNAInterface::set_forget_chains_and_interface ( bool  value )

inline

References forget_chains_and_interface_.

set_reference_pose()

void protocols::dna::RestrictDesignToProteinDNAInterface::set_reference_pose

(

PoseCOP

pose

)

References reference_pose_.

targeted_dna()

DnaDesignDefOPs const & protocols::dna::RestrictDesignToProteinDNAInterface::targeted_dna

(

)

const

References targeted_dna_.

Referenced by copy_targeted_dna().

Member Data Documentation

base_only_

bool protocols::dna::RestrictDesignToProteinDNAInterface::base_only_

private

Referenced by apply(), base_only(), parse_tag(), and set_base_only().

close_threshold_

core::Real protocols::dna::RestrictDesignToProteinDNAInterface::close_threshold_

private

Referenced by apply(), and parse_tag().

contact_threshold_

core::Real protocols::dna::RestrictDesignToProteinDNAInterface::contact_threshold_

private

Referenced by apply().

dna_chains_

DnaChainsOP protocols::dna::RestrictDesignToProteinDNAInterface::dna_chains_

mutableprivate

Referenced by apply(), copy_dna_chains(), and dna_chains().

forget_chains_and_interface_

bool protocols::dna::RestrictDesignToProteinDNAInterface::forget_chains_and_interface_

private

Referenced by apply(), forget_chains_and_interface(), parse_tag(), and set_forget_chains_and_interface().

interface_

DnaInterfaceFinderOP protocols::dna::RestrictDesignToProteinDNAInterface::interface_

mutableprivate

Referenced by apply(), copy_interface(), and interface().

reference_pose_

PoseCOP protocols::dna::RestrictDesignToProteinDNAInterface::reference_pose_

private

Referenced by apply(), reference_pose(), and set_reference_pose().

targeted_dna_

DnaDesignDefOPs protocols::dna::RestrictDesignToProteinDNAInterface::targeted_dna_

private

Referenced by apply(), copy_targeted_dna(), parse_tag(), and targeted_dna().

z_cutoff_

core::Real protocols::dna::RestrictDesignToProteinDNAInterface::z_cutoff_

mutableprivate

Referenced by apply(), and parse_tag().

---

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

• src/protocols/dna/RestrictDesignToProteinDNAInterface.hh
• src/protocols/dna/RestrictDesignToProteinDNAInterface.cc