protocols::task_operations::ProteinInterfaceDesignOperation Class Reference

#include <ProteinInterfaceDesignOperation.hh>

Inheritance diagram for protocols::task_operations::ProteinInterfaceDesignOperation:

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

parent

typedef RestrictOperationsBase protocols::task_operations::ProteinInterfaceDesignOperation::parent

Constructor & Destructor Documentation

ProteinInterfaceDesignOperation()

protocols::task_operations::ProteinInterfaceDesignOperation::ProteinInterfaceDesignOperation

(

)

~ProteinInterfaceDesignOperation()

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

overridedefault

Member Function Documentation

allow_all_aas()

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().

apply()

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::DesignAroundOperation::apply(), protocols::task_operations::PreventChainFromRepackingOperation::apply(), protocols::task_operations::RestrictChainToRepackingOperation::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(), protocols::task_operations::DesignAroundOperation::include_residue(), 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().

clone()

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.

design_all_aas()

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().

design_chain1()

void protocols::task_operations::ProteinInterfaceDesignOperation::design_chain1

(

bool const

design

)

References design_chain1_.

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

design_chain2()

void protocols::task_operations::ProteinInterfaceDesignOperation::design_chain2

(

bool const

design

)

References design_chain2_.

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

interface_distance_cutoff()

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().

jump() [1/2]

core::Size protocols::task_operations::ProteinInterfaceDesignOperation::jump

(

)

const

References jump_.

Referenced by apply(), and parse_tag().

jump() [2/2]

void protocols::task_operations::ProteinInterfaceDesignOperation::jump

(

core::Size const

j

)

References jump_.

keyname()

static std::string protocols::task_operations::ProteinInterfaceDesignOperation::keyname ( )

inlinestatic

Referenced by protocols::task_operations::SeqprofConsensusOperation::create_complex_type_generator(), protocols::task_operations::ProteinInterfaceDesignOperationCreator::keyname(), and provide_xml_schema().

modify_after_jump() [1/2]

bool protocols::task_operations::ProteinInterfaceDesignOperation::modify_after_jump ( ) const

inline

References modify_after_jump_.

Referenced by apply(), and parse_tag().

modify_after_jump() [2/2]

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

inline

References modify_after_jump_.

modify_before_jump() [1/2]

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

inline

References modify_before_jump_.

Referenced by apply(), and parse_tag().

modify_before_jump() [2/2]

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

inline

References modify_before_jump_.

parse_tag()

void protocols::task_operations::ProteinInterfaceDesignOperation::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 allow_all_aas(), design_all_aas(), design_chain1(), design_chain2(), interface_distance_cutoff(), jump(), modify_after_jump(), modify_before_jump(), repack_chain1(), and repack_chain2().

provide_xml_schema()

void protocols::task_operations::ProteinInterfaceDesignOperation::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd )

static

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

Referenced by protocols::task_operations::SeqprofConsensusOperation::create_complex_type_generator(), and protocols::task_operations::ProteinInterfaceDesignOperationCreator::provide_xml_schema().

repack_chain1()

void protocols::task_operations::ProteinInterfaceDesignOperation::repack_chain1

(

bool const

repack

)

References protocols::antibody::design::repack, and repack_chain1_.

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

repack_chain2()

void protocols::task_operations::ProteinInterfaceDesignOperation::repack_chain2

(

bool const

repack

)

References protocols::antibody::design::repack, and repack_chain2_.

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

Member Data Documentation

allow_all_aas_

bool protocols::task_operations::ProteinInterfaceDesignOperation::allow_all_aas_

private

Referenced by allow_all_aas(), and apply().

design_all_aas_

bool protocols::task_operations::ProteinInterfaceDesignOperation::design_all_aas_

private

Referenced by apply(), and design_all_aas().

design_chain1_

bool protocols::task_operations::ProteinInterfaceDesignOperation::design_chain1_

private

Referenced by apply(), and design_chain1().

design_chain2_

bool protocols::task_operations::ProteinInterfaceDesignOperation::design_chain2_

private

Referenced by apply(), and design_chain2().

interface_distance_cutoff_

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

private

Referenced by apply(), and interface_distance_cutoff().

jump_

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

private

Referenced by jump().

modify_after_jump_

bool protocols::task_operations::ProteinInterfaceDesignOperation::modify_after_jump_

private

Referenced by modify_after_jump().

modify_before_jump_

bool protocols::task_operations::ProteinInterfaceDesignOperation::modify_before_jump_

private

Referenced by modify_before_jump().

repack_chain1_

bool protocols::task_operations::ProteinInterfaceDesignOperation::repack_chain1_

private

Referenced by apply(), and repack_chain1().

repack_chain2_

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:

• src/protocols/task_operations/ProteinInterfaceDesignOperation.hh
• src/protocols/task_operations/ProteinInterfaceDesignOperation.cc