protocols::protein_interface_design::Revert Class Reference

#include <design_utils.hh>

Collaboration diagram for protocols::protein_interface_design::Revert:

Public Types
typedef core::scoring::ScoreFunction	ScoreFunction
typedef core::scoring::ScoreFunctionOP	ScoreFunctionOP
typedef core::scoring::ScoreFunctionCOP	ScoreFunctionCOP

Public Member Functions
	Revert (ScoreFunctionCOP scorefxn, core::Real const ddg_tolerance, core::Size ddg_cycles=5)
	Revert (Revert const &init)
void	apply (core::pose::Pose &pose_wt, core::pose::Pose &pose_des) const
virtual	~Revert ()

Private Attributes
core::scoring::ScoreFunctionOP	scorefxn_
core::Real	ddg_tolerance_
core::Size	ddg_cycles_

Detailed Description

class Revert takes in 'wt' and 'designed' poses and attempts to revert all substitutions in the design to their wt identities. Each substitution is tried separately in the context of the designed protein and reversions that don't adversely affect ddg are made. If the energy of the residue in the design is higher than 0, but the reversion did not succeed, Revert will attempt an Ala substitution.

Definition at line 79 of file design_utils.hh.

Member Typedef Documentation

typedef core::scoring::ScoreFunction protocols::protein_interface_design::Revert::ScoreFunction

Definition at line 82 of file design_utils.hh.

typedef core::scoring::ScoreFunctionCOP protocols::protein_interface_design::Revert::ScoreFunctionCOP

Definition at line 84 of file design_utils.hh.

typedef core::scoring::ScoreFunctionOP protocols::protein_interface_design::Revert::ScoreFunctionOP

Definition at line 83 of file design_utils.hh.

Constructor & Destructor Documentation

protocols::protein_interface_design::Revert::Revert ( ScoreFunctionCOP  scorefxn, core::Real const  ddg_tolerance, core::Size  ddg_cycles = 5  )

inline

Definition at line 86 of file design_utils.hh.

References ddg_cycles_, ddg_tolerance_, and scorefxn_.

protocols::protein_interface_design::Revert::Revert ( Revert const &  init)

inline

Definition at line 91 of file design_utils.hh.

References ddg_cycles_, ddg_tolerance_, and scorefxn_.

virtual protocols::protein_interface_design::Revert::~Revert ( )

inlinevirtual

Definition at line 97 of file design_utils.hh.

Member Function Documentation

void Revert::apply	(	core::pose::Pose &	pose_wt,
		core::pose::Pose &	pose_des
	)		const

Definition at line 191 of file design_utils.cc.

References core::conformation::Residue::aa(), core::chemical::aa_ala, core::pose::Pose::copy_segment(), ddG_cycles(), core::conformation::Residue::name3(), point_mutation(), core::pose::Pose::residue(), and core::TR().

Member Data Documentation

core::Size protocols::protein_interface_design::Revert::ddg_cycles_

private

Definition at line 101 of file design_utils.hh.

Referenced by Revert().

core::Real protocols::protein_interface_design::Revert::ddg_tolerance_

private

Definition at line 100 of file design_utils.hh.

Referenced by Revert().

core::scoring::ScoreFunctionOP protocols::protein_interface_design::Revert::scorefxn_

private

Definition at line 97 of file design_utils.hh.

Referenced by Revert().

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

• src/protocols/protein_interface_design/design_utils.hh
• src/protocols/protein_interface_design/design_utils.cc