protocols::protein_interface_design::Revert Class Reference

#include <design_utils.hh>

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 ()=default

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.

Member Typedef Documentation

ScoreFunction

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

ScoreFunctionCOP

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

ScoreFunctionOP

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

Constructor & Destructor Documentation

Revert() [1/2]

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

inline

References ddg_cycles_, ddg_tolerance_, and scorefxn_.

Revert() [2/2]

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

inline

References ddg_cycles_, ddg_tolerance_, core::init::init(), and scorefxn_.

~Revert()

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

virtualdefault

Member Function Documentation

apply()

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

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

Member Data Documentation

ddg_cycles_

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

private

Referenced by Revert().

ddg_tolerance_

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

private

Referenced by Revert().

scorefxn_

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

private

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