Rosetta 3.4
Public Types | Public Member Functions
protocols::dna::RestrictDesignToProteinDNAInterface Class Reference

#include <RestrictDesignToProteinDNAInterface.hh>

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List of all members.

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 Member Functions

 RestrictDesignToProteinDNAInterface ()
virtual ~RestrictDesignToProteinDNAInterface ()
virtual TaskOperationOP clone () const
 Create another task operation of the type matching the most-derived version of the class.
virtual void apply (Pose const &pose, PackerTask &ptask) const
 determines the DNA interface residues and informs a PackerTask of their appropriate packing behavior
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.

Member Typedef Documentation


Constructor & Destructor Documentation

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

Referenced by clone().

protocols::dna::RestrictDesignToProteinDNAInterface::~RestrictDesignToProteinDNAInterface ( ) [virtual]

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.

References core::chemical::ResidueType::aa(), protocols::dna::DnaPosition::bottom(), core::pose::Pose::chain(), protocols::dna::DnaNeighbor::close(), core::pose::Pose::constraint_set(), protocols::dna::DnaNeighbor::contact(), protocols::dna::dna_comp_name_str(), core::sequence::end, core::pose::PDBPoseMap::find(), protocols::dna::find_basepairs(), core::pack::task::ResidueLevelTask::has_behavior(), 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(), core::pose::Pose::residue(), core::pack::task::PackerTask::residue_task(), core::pose::Pose::residue_type(), core::conformation::Residue::residue_type_set(), protocols::dna::DnaPosition::top(), core::pack::task::PackerTask::total_residue(), core::pose::Pose::total_residue(), and protocols::dna::TR().

bool protocols::dna::RestrictDesignToProteinDNAInterface::base_only ( ) const [inline]
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.

References RestrictDesignToProteinDNAInterface().

void protocols::dna::RestrictDesignToProteinDNAInterface::copy_dna_chains ( DnaChainsCOP  chains)
void protocols::dna::RestrictDesignToProteinDNAInterface::copy_interface ( DnaInterfaceFinderCOP  interface)
void protocols::dna::RestrictDesignToProteinDNAInterface::copy_targeted_dna ( DnaDesignDefOPs const &  targeted_dna)

References targeted_dna().

DnaChainsCOP protocols::dna::RestrictDesignToProteinDNAInterface::dna_chains ( ) const
bool protocols::dna::RestrictDesignToProteinDNAInterface::forget_chains_and_interface ( ) const [inline]
DnaInterfaceFinderCOP protocols::dna::RestrictDesignToProteinDNAInterface::interface ( ) const
void protocols::dna::RestrictDesignToProteinDNAInterface::parse_tag ( TagPtr  tag) [virtual]
PoseCOP protocols::dna::RestrictDesignToProteinDNAInterface::reference_pose ( ) const
void protocols::dna::RestrictDesignToProteinDNAInterface::set_base_only ( bool  value) [inline]
void protocols::dna::RestrictDesignToProteinDNAInterface::set_forget_chains_and_interface ( bool  value) [inline]
void protocols::dna::RestrictDesignToProteinDNAInterface::set_reference_pose ( PoseCOP  pose)
DnaDesignDefOPs const & protocols::dna::RestrictDesignToProteinDNAInterface::targeted_dna ( ) const

Referenced by copy_targeted_dna().


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