#include <ProteinInterfaceDesignOperation.hh>

Inheritance diagram for protocols::toolbox::task_operations::ProteinInterfaceDesignOperation:

Collaboration diagram for protocols::toolbox::task_operations::ProteinInterfaceDesignOperation:

Public Types
typedef RestrictOperationsBase	parent

Public Types inherited from protocols::toolbox::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::TagPtr	TagPtr

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

virtual	~ProteinInterfaceDesignOperation ()

virtual TaskOperationOP	clone () const
	Create another task operation of the type matching the most-derived version of the class. More...

virtual void	apply (core::pose::Pose const &, core::pack::task::PackerTask &) const
	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...

virtual void	parse_tag (TagPtr)
	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::toolbox::task_operations::RestrictOperationsBase
	RestrictOperationsBase ()

virtual	~RestrictOperationsBase ()

Public Member Functions inherited from core::pack::task::operation::TaskOperation
virtual	~TaskOperation ()

virtual void	parse_def (utility::lua::LuaObject const &def)

Additional Inherited Members
Protected Member Functions inherited from protocols::toolbox::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.

Definition at line 40 of file ProteinInterfaceDesignOperation.hh.

Member Typedef Documentation

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

Definition at line 43 of file ProteinInterfaceDesignOperation.hh.

Constructor & Destructor Documentation

protocols::toolbox::task_operations::ProteinInterfaceDesignOperation::ProteinInterfaceDesignOperation ( )

Definition at line 56 of file ProteinInterfaceDesignOperation.cc.

Referenced by clone().

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

virtual

Definition at line 69 of file ProteinInterfaceDesignOperation.cc.

Member Function Documentation

void protocols::toolbox::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

Definition at line 182 of file ProteinInterfaceDesignOperation.cc.

References allow_all_aas_.

Referenced by parse_tag().

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

virtual

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::toolbox::task_operations::RestrictOperationsBase.

Definition at line 85 of file ProteinInterfaceDesignOperation.cc.

References core::conformation::Residue::aa(), core::chemical::aa_cys, core::chemical::aa_gly, core::chemical::aa_pro, allow_all_aas_, protocols::toolbox::task_operations::RestrictChainToRepackingOperation::apply(), protocols::toolbox::task_operations::PreventChainFromRepackingOperation::apply(), core::pack::task::operation::OperateOnCertainResidues::apply(), core::pack::task::operation::NoRepackDisulfides::apply(), core::pack::task::operation::RestrictAbsentCanonicalAAS::apply(), protocols::toolbox::task_operations::PreventChainFromRepackingOperation::chain(), protocols::toolbox::task_operations::RestrictChainToRepackingOperation::chain(), core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), design_all_aas_, design_chain1_, design_chain2_, protocols::toolbox::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(), and core::pose::Pose::total_residue().

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

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

virtual

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

Implements protocols::toolbox::task_operations::RestrictOperationsBase.

Definition at line 77 of file ProteinInterfaceDesignOperation.cc.

References ProteinInterfaceDesignOperation().

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

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

Definition at line 187 of file ProteinInterfaceDesignOperation.cc.

References design_all_aas_.

Referenced by parse_tag().

void protocols::toolbox::task_operations::ProteinInterfaceDesignOperation::design_chain1 ( bool const design)

Definition at line 171 of file ProteinInterfaceDesignOperation.cc.

References design_chain1_.

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

void protocols::toolbox::task_operations::ProteinInterfaceDesignOperation::design_chain2 ( bool const design)

Definition at line 176 of file ProteinInterfaceDesignOperation.cc.

References design_chain2_.

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

void protocols::toolbox::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.

Definition at line 192 of file ProteinInterfaceDesignOperation.cc.

References interface_distance_cutoff_.

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

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

Definition at line 197 of file ProteinInterfaceDesignOperation.cc.

References jump_.

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

Definition at line 202 of file ProteinInterfaceDesignOperation.cc.

References jump_.

Referenced by apply(), and parse_tag().

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

inline

Definition at line 73 of file ProteinInterfaceDesignOperation.hh.

References modify_after_jump_.

Referenced by apply(), and parse_tag().

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

inline

Definition at line 74 of file ProteinInterfaceDesignOperation.hh.

References modify_after_jump_.

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

inline

Definition at line 71 of file ProteinInterfaceDesignOperation.hh.

References modify_before_jump_.

Referenced by apply(), and parse_tag().

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

inline

Definition at line 72 of file ProteinInterfaceDesignOperation.hh.

References modify_before_jump_.

void protocols::toolbox::task_operations::ProteinInterfaceDesignOperation::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 208 of file ProteinInterfaceDesignOperation.cc.

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().

void protocols::toolbox::task_operations::ProteinInterfaceDesignOperation::repack_chain1 ( bool const repack)

Definition at line 161 of file ProteinInterfaceDesignOperation.cc.

References repack_chain1_.

Referenced by protocols::protein_interface_design::movers::HotspotDisjointedFoldTreeMover::apply(), parse_tag(), and protocols::simple_moves::DesignRepackMover::setup_packer_and_movemap().

void protocols::toolbox::task_operations::ProteinInterfaceDesignOperation::repack_chain2 ( bool const repack)

Definition at line 166 of file ProteinInterfaceDesignOperation.cc.

References repack_chain2_.

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

Member Data Documentation

bool protocols::toolbox::task_operations::ProteinInterfaceDesignOperation::allow_all_aas_

private

Definition at line 79 of file ProteinInterfaceDesignOperation.hh.

Referenced by allow_all_aas(), and apply().

bool protocols::toolbox::task_operations::ProteinInterfaceDesignOperation::design_all_aas_

private

Definition at line 79 of file ProteinInterfaceDesignOperation.hh.

Referenced by apply(), and design_all_aas().

bool protocols::toolbox::task_operations::ProteinInterfaceDesignOperation::design_chain1_

private

Definition at line 78 of file ProteinInterfaceDesignOperation.hh.

Referenced by apply(), and design_chain1().

bool protocols::toolbox::task_operations::ProteinInterfaceDesignOperation::design_chain2_

private

Definition at line 78 of file ProteinInterfaceDesignOperation.hh.

Referenced by apply(), and design_chain2().

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

private

Definition at line 80 of file ProteinInterfaceDesignOperation.hh.

Referenced by apply(), and interface_distance_cutoff().

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

private

Definition at line 81 of file ProteinInterfaceDesignOperation.hh.

Referenced by jump().

bool protocols::toolbox::task_operations::ProteinInterfaceDesignOperation::modify_after_jump_

private

Definition at line 82 of file ProteinInterfaceDesignOperation.hh.

Referenced by modify_after_jump().

bool protocols::toolbox::task_operations::ProteinInterfaceDesignOperation::modify_before_jump_

private

Definition at line 82 of file ProteinInterfaceDesignOperation.hh.

Referenced by modify_before_jump().

bool protocols::toolbox::task_operations::ProteinInterfaceDesignOperation::repack_chain1_

private

Definition at line 77 of file ProteinInterfaceDesignOperation.hh.

Referenced by apply(), and repack_chain1().

bool protocols::toolbox::task_operations::ProteinInterfaceDesignOperation::repack_chain2_

private

Definition at line 77 of file ProteinInterfaceDesignOperation.hh.

Referenced by apply(), and repack_chain2().

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

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

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_

Public Types

Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation