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protocols::dna::RestrictDesignToProteinDNAInterface Class Reference

#include <RestrictDesignToProteinDNAInterface.hh>

Inheritance diagram for protocols::dna::RestrictDesignToProteinDNAInterface:
Inheritance graph
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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 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 Does this task_operation indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)?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 ()
 

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

Constructor & Destructor Documentation

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

Member Function Documentation

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(), 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::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::chemical::ResidueTypeFinder::name3(), 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::pose::Pose::residue_type_set_for_pose(), 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_.

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

References base_only_.

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.

void protocols::dna::RestrictDesignToProteinDNAInterface::copy_dna_chains ( DnaChainsCOP  chains)

References dna_chains_.

void protocols::dna::RestrictDesignToProteinDNAInterface::copy_interface ( DnaInterfaceFinderCOP  interface)

References interface_.

void protocols::dna::RestrictDesignToProteinDNAInterface::copy_targeted_dna ( DnaDesignDefOPs const &  targeted_dna)

References targeted_dna(), and targeted_dna_.

DnaChainsCOP protocols::dna::RestrictDesignToProteinDNAInterface::dna_chains ( ) const

References dna_chains_.

bool protocols::dna::RestrictDesignToProteinDNAInterface::forget_chains_and_interface ( ) const
inline
DnaInterfaceFinderCOP protocols::dna::RestrictDesignToProteinDNAInterface::interface ( ) const

References interface_.

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

Referenced by provide_xml_schema().

void protocols::dna::RestrictDesignToProteinDNAInterface::parse_tag ( TagCOP  tag,
DataMap  
)
overridevirtual
void protocols::dna::RestrictDesignToProteinDNAInterface::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
PoseCOP protocols::dna::RestrictDesignToProteinDNAInterface::reference_pose ( ) const

References reference_pose_.

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

References base_only_.

void protocols::dna::RestrictDesignToProteinDNAInterface::set_forget_chains_and_interface ( bool  value)
inline
void protocols::dna::RestrictDesignToProteinDNAInterface::set_reference_pose ( PoseCOP  pose)

References reference_pose_.

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

References targeted_dna_.

Referenced by copy_targeted_dna().

Member Data Documentation

bool protocols::dna::RestrictDesignToProteinDNAInterface::base_only_
private
core::Real protocols::dna::RestrictDesignToProteinDNAInterface::close_threshold_
private

Referenced by apply(), and parse_tag().

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

Referenced by apply().

DnaChainsOP protocols::dna::RestrictDesignToProteinDNAInterface::dna_chains_
mutableprivate

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

bool protocols::dna::RestrictDesignToProteinDNAInterface::forget_chains_and_interface_
private
DnaInterfaceFinderOP protocols::dna::RestrictDesignToProteinDNAInterface::interface_
mutableprivate

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

PoseCOP protocols::dna::RestrictDesignToProteinDNAInterface::reference_pose_
private
DnaDesignDefOPs protocols::dna::RestrictDesignToProteinDNAInterface::targeted_dna_
private
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: