protocols::dna::RestrictDesignToProteinDNAInterface Class Reference

#include <RestrictDesignToProteinDNAInterface.hh>

Inheritance diagram for protocols::dna::RestrictDesignToProteinDNAInterface:

Collaboration 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::TagPtr	TagPtr
typedef pose::Pose	Pose

Public Member Functions
	RestrictDesignToProteinDNAInterface ()
virtual	~RestrictDesignToProteinDNAInterface ()
virtual TaskOperationOP	clone () const
	Create another task operation of the type matching the most-derived version of the class. More...
virtual void	apply (Pose const &pose, PackerTask &ptask) const
	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
virtual void	parse_tag (TagPtr)
	Used to parse an xml-like tag to load parameters and properties. More...
Public Member Functions inherited from core::pack::task::operation::TaskOperation
virtual	~TaskOperation ()
virtual void	parse_def (utility::lua::LuaObject const &def)

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_

Detailed Description

Definition at line 34 of file RestrictDesignToProteinDNAInterface.hh.

Member Typedef Documentation

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

Definition at line 41 of file RestrictDesignToProteinDNAInterface.hh.

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

Definition at line 42 of file RestrictDesignToProteinDNAInterface.hh.

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

Definition at line 37 of file RestrictDesignToProteinDNAInterface.hh.

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

Definition at line 38 of file RestrictDesignToProteinDNAInterface.hh.

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

Definition at line 39 of file RestrictDesignToProteinDNAInterface.hh.

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

Definition at line 40 of file RestrictDesignToProteinDNAInterface.hh.

Constructor & Destructor Documentation

protocols::dna::RestrictDesignToProteinDNAInterface::RestrictDesignToProteinDNAInterface

(

)

Definition at line 75 of file RestrictDesignToProteinDNAInterface.cc.

Referenced by clone().

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

virtual

Definition at line 87 of file RestrictDesignToProteinDNAInterface.cc.

Member Function Documentation

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

virtual

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

RestrictDesignToProteinDNAInterface::apply

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.

Definition at line 165 of file RestrictDesignToProteinDNAInterface.cc.

References core::chemical::ResidueType::aa(), base_only_, 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::pack::task::ResidueLevelTask::has_behavior(), interface_, core::chemical::ResidueType::is_DNA(), core::chemical::ResidueType::is_protein(), core::conformation::Residue::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::conformation::Residue::residue_type_set(), targeted_dna_, protocols::dna::DnaPosition::top(), core::pack::task::PackerTask::total_residue(), core::pose::Pose::total_residue(), protocols::dna::TR(), and z_cutoff_.

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

inline

Definition at line 65 of file RestrictDesignToProteinDNAInterface.hh.

References base_only_.

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

virtual

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

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

Definition at line 89 of file RestrictDesignToProteinDNAInterface.cc.

References RestrictDesignToProteinDNAInterface().

void protocols::dna::RestrictDesignToProteinDNAInterface::copy_dna_chains

(

DnaChainsCOP

chains)

Definition at line 95 of file RestrictDesignToProteinDNAInterface.cc.

References dna_chains_.

void protocols::dna::RestrictDesignToProteinDNAInterface::copy_interface

(

DnaInterfaceFinderCOP

interface)

Definition at line 113 of file RestrictDesignToProteinDNAInterface.cc.

References interface_.

void protocols::dna::RestrictDesignToProteinDNAInterface::copy_targeted_dna

(

DnaDesignDefOPs const &

targeted_dna)

Definition at line 104 of file RestrictDesignToProteinDNAInterface.cc.

References targeted_dna(), and targeted_dna_.

DnaChainsCOP protocols::dna::RestrictDesignToProteinDNAInterface::dna_chains

(

)

const

Definition at line 101 of file RestrictDesignToProteinDNAInterface.cc.

References dna_chains_.

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

inline

Definition at line 68 of file RestrictDesignToProteinDNAInterface.hh.

References forget_chains_and_interface_.

DnaInterfaceFinderCOP protocols::dna::RestrictDesignToProteinDNAInterface::interface

(

)

const

Definition at line 119 of file RestrictDesignToProteinDNAInterface.cc.

References interface_.

void protocols::dna::RestrictDesignToProteinDNAInterface::parse_tag ( TagPtr  tag)

virtual

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

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

Definition at line 131 of file RestrictDesignToProteinDNAInterface.cc.

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_.

PoseCOP protocols::dna::RestrictDesignToProteinDNAInterface::reference_pose

(

)

const

Definition at line 128 of file RestrictDesignToProteinDNAInterface.cc.

References reference_pose_.

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

inline

Definition at line 64 of file RestrictDesignToProteinDNAInterface.hh.

References base_only_.

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

inline

Definition at line 67 of file RestrictDesignToProteinDNAInterface.hh.

References forget_chains_and_interface_.

void protocols::dna::RestrictDesignToProteinDNAInterface::set_reference_pose

(

PoseCOP

pose)

Definition at line 122 of file RestrictDesignToProteinDNAInterface.cc.

References reference_pose_.

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

(

)

const

Definition at line 110 of file RestrictDesignToProteinDNAInterface.cc.

References targeted_dna_.

Referenced by copy_targeted_dna().

Member Data Documentation

bool protocols::dna::RestrictDesignToProteinDNAInterface::base_only_

private

Definition at line 78 of file RestrictDesignToProteinDNAInterface.hh.

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

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

private

Definition at line 81 of file RestrictDesignToProteinDNAInterface.hh.

Referenced by apply(), and parse_tag().

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

private

Definition at line 81 of file RestrictDesignToProteinDNAInterface.hh.

Referenced by apply().

DnaChainsOP protocols::dna::RestrictDesignToProteinDNAInterface::dna_chains_

mutableprivate

Definition at line 74 of file RestrictDesignToProteinDNAInterface.hh.

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

bool protocols::dna::RestrictDesignToProteinDNAInterface::forget_chains_and_interface_

private

Definition at line 79 of file RestrictDesignToProteinDNAInterface.hh.

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

DnaInterfaceFinderOP protocols::dna::RestrictDesignToProteinDNAInterface::interface_

mutableprivate

Definition at line 76 of file RestrictDesignToProteinDNAInterface.hh.

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

PoseCOP protocols::dna::RestrictDesignToProteinDNAInterface::reference_pose_

private

Definition at line 77 of file RestrictDesignToProteinDNAInterface.hh.

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

DnaDesignDefOPs protocols::dna::RestrictDesignToProteinDNAInterface::targeted_dna_

private

Definition at line 75 of file RestrictDesignToProteinDNAInterface.hh.

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

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

mutableprivate

Definition at line 80 of file RestrictDesignToProteinDNAInterface.hh.

Referenced by apply(), and parse_tag().

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

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