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Public Types | Public Member Functions | Static Public Member Functions | Private Attributes | List of all members
protocols::task_operations::ProteinInterfaceDesignOperation Class Reference

#include <ProteinInterfaceDesignOperation.hh>

Inheritance diagram for protocols::task_operations::ProteinInterfaceDesignOperation:
Inheritance graph
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Public Types

typedef RestrictOperationsBase parent
 
- Public Types inherited from protocols::task_operations::RestrictOperationsBase
typedef
core::pack::task::operation::TaskOperation 
TaskOperation
 
typedef
core::pack::task::operation::TaskOperationOP 
TaskOperationOP
 
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

 ProteinInterfaceDesignOperation ()
 
void repack_chain1 (bool const repack)
 
void repack_chain2 (bool const repack)
 
void design_chain1 (bool const design)
 
void design_chain2 (bool const design)
 
void allow_all_aas (bool const allow)
 allow all amino acids to be designed at all positions, do not exclude C, G, P More...
 
void design_all_aas (bool const design_all)
 allow design of all residues on input pose, do not exclude G,P More...
 
void interface_distance_cutoff (core::Real const dist)
 distance cutoff for atom distance in an interface. All residues an atoms less than the distance cutoff from an atom in the other chain are defined as interface. More...
 
void jump (core::Size const j)
 
core::Size jump () const
 
 ~ProteinInterfaceDesignOperation () override
 
TaskOperationOP clone () const override
 Create another task operation of the type matching the most-derived version of the class. More...
 
void apply (core::pose::Pose const &, core::pack::task::PackerTask &) const override
 the default taskoperation for protein-interface design. Sets up which chains to repack/design disable disulfides, prolines and glycines from design, restrict designable positions to all but pro/gly/cys More...
 
void parse_tag (TagCOP, DataMap &) override
 Used to parse an xml-like tag to load parameters and properties. More...
 
bool modify_before_jump () const
 
void modify_before_jump (bool const m)
 
bool modify_after_jump () const
 
void modify_after_jump (bool const m)
 
- Public Member Functions inherited from protocols::task_operations::RestrictOperationsBase
 RestrictOperationsBase ()
 
 ~RestrictOperationsBase () override
 
- 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

bool repack_chain1_
 
bool repack_chain2_
 
bool design_chain1_
 
bool design_chain2_
 
bool allow_all_aas_
 
bool design_all_aas_
 
core::Real interface_distance_cutoff_
 
core::Size jump_
 
bool modify_before_jump_
 
bool modify_after_jump_
 

Additional Inherited Members

- Protected Member Functions inherited from protocols::task_operations::RestrictOperationsBase
void run_calculator (core::pose::Pose const &pose, std::string const &calculator, std::string const &calculation, utility::vector1_bool &residues) const
 this is the only real function - it takes a calculator name and calculation, and a PackerTask-compatible vector, and flips booleans in the vector according to the calculator More...
 

Detailed Description

this class is a TaskOperation to prevent repacking of residues not near an interface.

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::task_operations::ProteinInterfaceDesignOperation::ProteinInterfaceDesignOperation ( )
protocols::task_operations::ProteinInterfaceDesignOperation::~ProteinInterfaceDesignOperation ( )
overridedefault

Member Function Documentation

void protocols::task_operations::ProteinInterfaceDesignOperation::allow_all_aas ( bool const  allow)

allow all amino acids to be designed at all positions, do not exclude C, G, P

References allow_all_aas_.

Referenced by parse_tag().

void protocols::task_operations::ProteinInterfaceDesignOperation::apply ( core::pose::Pose const &  pose,
core::pack::task::PackerTask task 
) const
overridevirtual

the default taskoperation for protein-interface design. Sets up which chains to repack/design disable disulfides, prolines and glycines from design, restrict designable positions to all but pro/gly/cys

Implements protocols::task_operations::RestrictOperationsBase.

References core::conformation::Residue::aa(), core::chemical::aa_cys, core::chemical::aa_gly, core::chemical::aa_pro, allow_all_aas_, protocols::task_operations::RestrictChainToRepackingOperation::apply(), protocols::task_operations::PreventChainFromRepackingOperation::apply(), core::pack::task::operation::OperateOnCertainResidues::apply(), core::pack::task::operation::NoRepackDisulfides::apply(), core::pack::task::operation::RestrictAbsentCanonicalAAS::apply(), protocols::task_operations::PreventChainFromRepackingOperation::chain(), protocols::task_operations::RestrictChainToRepackingOperation::chain(), core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), design_all_aas_, design_chain1_, design_chain2_, protocols::task_operations::DesignAroundOperation::design_shell(), interface_distance_cutoff_, jump(), modify_after_jump(), modify_before_jump(), core::chemical::num_canonical_aas, core::conformation::Conformation::num_chains(), core::pack::task::operation::OperateOnCertainResidues::op(), repack_chain1_, repack_chain2_, core::pose::Pose::residue(), core::pack::task::operation::OperateOnCertainResidues::residue_indices(), core::pose::Pose::size(), and protocols::task_operations::TR().

Referenced by protocols::calc_taskop_movers::DesignRepackMover::setup_packer_and_movemap().

core::pack::task::operation::TaskOperationOP protocols::task_operations::ProteinInterfaceDesignOperation::clone ( ) const
overridevirtual

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

Implements protocols::task_operations::RestrictOperationsBase.

void protocols::task_operations::ProteinInterfaceDesignOperation::design_all_aas ( bool const  design_all)

allow design of all residues on input pose, do not exclude G,P

References design_all_aas_.

Referenced by parse_tag().

void protocols::task_operations::ProteinInterfaceDesignOperation::design_chain1 ( bool const  design)
void protocols::task_operations::ProteinInterfaceDesignOperation::design_chain2 ( bool const  design)
void protocols::task_operations::ProteinInterfaceDesignOperation::interface_distance_cutoff ( core::Real const  dist)

distance cutoff for atom distance in an interface. All residues an atoms less than the distance cutoff from an atom in the other chain are defined as interface.

References interface_distance_cutoff_.

Referenced by parse_tag(), and protocols::calc_taskop_movers::DesignRepackMover::setup_packer_and_movemap().

void protocols::task_operations::ProteinInterfaceDesignOperation::jump ( core::Size const  j)

References jump_.

core::Size protocols::task_operations::ProteinInterfaceDesignOperation::jump ( ) const

References jump_.

Referenced by apply(), and parse_tag().

static std::string protocols::task_operations::ProteinInterfaceDesignOperation::keyname ( )
inlinestatic
bool protocols::task_operations::ProteinInterfaceDesignOperation::modify_after_jump ( ) const
inline

References modify_after_jump_.

Referenced by apply(), and parse_tag().

void protocols::task_operations::ProteinInterfaceDesignOperation::modify_after_jump ( bool const  m)
inline

References modify_after_jump_.

bool protocols::task_operations::ProteinInterfaceDesignOperation::modify_before_jump ( ) const
inline

References modify_before_jump_.

Referenced by apply(), and parse_tag().

void protocols::task_operations::ProteinInterfaceDesignOperation::modify_before_jump ( bool const  m)
inline

References modify_before_jump_.

void protocols::task_operations::ProteinInterfaceDesignOperation::parse_tag ( TagCOP  tag,
DataMap  
)
overridevirtual
void protocols::task_operations::ProteinInterfaceDesignOperation::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::task_operations::ProteinInterfaceDesignOperation::repack_chain1 ( bool const  repack)
void protocols::task_operations::ProteinInterfaceDesignOperation::repack_chain2 ( bool const  repack)

Member Data Documentation

bool protocols::task_operations::ProteinInterfaceDesignOperation::allow_all_aas_
private

Referenced by allow_all_aas(), and apply().

bool protocols::task_operations::ProteinInterfaceDesignOperation::design_all_aas_
private

Referenced by apply(), and design_all_aas().

bool protocols::task_operations::ProteinInterfaceDesignOperation::design_chain1_
private

Referenced by apply(), and design_chain1().

bool protocols::task_operations::ProteinInterfaceDesignOperation::design_chain2_
private

Referenced by apply(), and design_chain2().

core::Real protocols::task_operations::ProteinInterfaceDesignOperation::interface_distance_cutoff_
private

Referenced by apply(), and interface_distance_cutoff().

core::Size protocols::task_operations::ProteinInterfaceDesignOperation::jump_
private

Referenced by jump().

bool protocols::task_operations::ProteinInterfaceDesignOperation::modify_after_jump_
private

Referenced by modify_after_jump().

bool protocols::task_operations::ProteinInterfaceDesignOperation::modify_before_jump_
private

Referenced by modify_before_jump().

bool protocols::task_operations::ProteinInterfaceDesignOperation::repack_chain1_
private

Referenced by apply(), and repack_chain1().

bool protocols::task_operations::ProteinInterfaceDesignOperation::repack_chain2_
private

Referenced by apply(), and repack_chain2().


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