protocols::design_opt::PointMutationCalculator Class Reference

#include <PointMutationCalculator.hh>

Inheritance diagram for protocols::design_opt::PointMutationCalculator:

Public Types
typedef core::pose::Pose	Pose

Public Member Functions
	PointMutationCalculator ()
	default ctor More...
	PointMutationCalculator (core::pack::task::TaskFactoryOP task_factory, core::scoring::ScoreFunctionOP scorefxn, protocols::moves::MoverOP relax_mover, utility::vector1< protocols::filters::FilterOP > filters, utility::vector1< std::string > sample_types, bool dump_pdb=false, bool rtmin=false, bool parallel=false, core::Real design_shell=-1.0, core::Real repack_shell=8.0)
	PointMutationCalculator (core::pack::task::TaskFactoryOP task_factory, core::scoring::ScoreFunctionOP scorefxn, protocols::moves::MoverOP relax_mover, protocols::filters::FilterOP filter, std::string sample_type="low", bool dump_pdb=false, bool rtmin=false, bool parallel=false, core::Real design_shell=-1.0, core::Real repack_shell=8.0)
	~PointMutationCalculator () override
void	mutate_and_relax (core::pose::Pose &pose, core::Size const &resi, core::chemical::AA const &target_aa)
void	mutate_and_relax (core::pose::Pose &pose, core::Size const &resi, core::chemical::AA const &target_aa, protocols::minimization_packing::GreenPackerOP green_packer)
void	eval_filters (core::pose::Pose &pose, bool &filter_pass, utility::vector1< core::Real > &vals)
void	calc_point_mut_filters (Pose const &start_pose, utility::vector1< std::pair< core::Size, utility::vector1< std::pair< core::chemical::AA, utility::vector1< core::Real > > > > > &seqpos_aa_vals_vec)
void	calc_point_mut_filters (Pose const &start_pose, utility::vector1< std::pair< core::Size, utility::vector1< std::pair< core::chemical::AA, core::Real > > > > &seqpos_aa_val_vec)
protocols::design_opt::PointMutationCalculatorOP	clone () const
core::pack::task::TaskFactoryOP	task_factory () const
void	task_factory (core::pack::task::TaskFactoryOP task_factory)
core::scoring::ScoreFunctionOP	scorefxn () const
void	scorefxn (core::scoring::ScoreFunctionOP scorefxn)
utility::vector1 < protocols::filters::FilterOP >	filters () const
void	filters (utility::vector1< protocols::filters::FilterOP > filters)
protocols::moves::MoverOP	relax_mover () const
void	relax_mover (protocols::moves::MoverOP relax_mover)
bool	dump_pdb () const
void	dump_pdb (bool const dump_pdb)
utility::vector1< std::string >	sample_types () const
void	sample_types (utility::vector1< std::string > const &sample_types)
void	rtmin (bool const r)
bool	rtmin () const
void	parallel (bool const r)
bool	parallel () const
void	set_design_shell (core::Real dz_shell)
void	set_repack_shell (core::Real rp_shell)

Private Attributes
core::pack::task::TaskFactoryOP	task_factory_
core::scoring::ScoreFunctionOP	scorefxn_
utility::vector1 < protocols::filters::FilterOP >	filters_
protocols::moves::MoverOP	relax_mover_
utility::vector1< std::string >	sample_types_
bool	dump_pdb_
bool	rtmin_
bool	parallel_
core::Real	design_shell_
core::Real	repack_shell_

Member Typedef Documentation

typedef core::pose::Pose protocols::design_opt::PointMutationCalculator::Pose

Constructor & Destructor Documentation

protocols::design_opt::PointMutationCalculator::PointMutationCalculator

(

)

default ctor

protocols::design_opt::PointMutationCalculator::PointMutationCalculator	(	core::pack::task::TaskFactoryOP	task_factory,
		core::scoring::ScoreFunctionOP	scorefxn,
		protocols::moves::MoverOP	relax_mover,
		utility::vector1< protocols::filters::FilterOP >	filters,
		utility::vector1< std::string >	sample_types,
		bool	dump_pdb = false,
		bool	rtmin = false,
		bool	parallel = false,
		core::Real	design_shell = -1.0,
		core::Real	repack_shell = 8.0
	)

References design_shell_, dump_pdb(), dump_pdb_, filters(), filters_, parallel(), parallel_, relax_mover(), relax_mover_, repack_shell_, rtmin(), rtmin_, sample_types(), sample_types_, scorefxn(), scorefxn_, task_factory(), task_factory_, and protocols::design_opt::TR().

protocols::design_opt::PointMutationCalculator::PointMutationCalculator	(	core::pack::task::TaskFactoryOP	task_factory,
		core::scoring::ScoreFunctionOP	scorefxn,
		protocols::moves::MoverOP	relax_mover,
		protocols::filters::FilterOP	filter,
		std::string	sample_type = "low",
		bool	dump_pdb = false,
		bool	rtmin = false,
		bool	parallel = false,
		core::Real	design_shell = -1.0,
		core::Real	repack_shell = 8.0
	)

References design_shell_, dump_pdb(), dump_pdb_, filters(), filters_, parallel(), parallel_, relax_mover(), relax_mover_, repack_shell_, rtmin(), rtmin_, sample_types(), sample_types_, scorefxn(), scorefxn_, task_factory(), task_factory_, and protocols::design_opt::TR().

protocols::design_opt::PointMutationCalculator::~PointMutationCalculator ( )

overridedefault

Member Function Documentation

void protocols::design_opt::PointMutationCalculator::calc_point_mut_filters	(	Pose const &	start_pose,
		utility::vector1< std::pair< core::Size, utility::vector1< std::pair< core::chemical::AA, utility::vector1< core::Real > > > > > &	seqpos_aa_vals_vec
	)

void protocols::design_opt::PointMutationCalculator::calc_point_mut_filters	(	Pose const &	start_pose,
		utility::vector1< std::pair< core::Size, utility::vector1< std::pair< core::chemical::AA, core::Real > > > > &	seqpos_aa_val_vec
	)

protocols::design_opt::PointMutationCalculatorOP protocols::design_opt::PointMutationCalculator::clone

(

)

const

bool protocols::design_opt::PointMutationCalculator::dump_pdb

(

)

const

References dump_pdb_.

Referenced by dump_pdb(), and PointMutationCalculator().

void protocols::design_opt::PointMutationCalculator::dump_pdb

(

bool const

dump_pdb

)

References dump_pdb(), and dump_pdb_.

void protocols::design_opt::PointMutationCalculator::eval_filters	(	core::pose::Pose &	pose,
		bool &	filter_pass,
		utility::vector1< core::Real > &	vals
	)

References protocols::design_opt::TR(), and protocols::hybridization::val.

vector1< protocols::filters::FilterOP > protocols::design_opt::PointMutationCalculator::filters

(

)

const

References filters_.

Referenced by filters(), and PointMutationCalculator().

void protocols::design_opt::PointMutationCalculator::filters

(

utility::vector1< protocols::filters::FilterOP >

filters

)

References filters(), and filters_.

void protocols::design_opt::PointMutationCalculator::mutate_and_relax	(	core::pose::Pose &	pose,
		core::Size const &	resi,
		core::chemical::AA const &	target_aa
	)

void protocols::design_opt::PointMutationCalculator::mutate_and_relax	(	core::pose::Pose &	pose,
		core::Size const &	resi,
		core::chemical::AA const &	target_aa,
		protocols::minimization_packing::GreenPackerOP	green_packer
	)

void protocols::design_opt::PointMutationCalculator::parallel

(

bool const

r

)

References parallel_.

bool protocols::design_opt::PointMutationCalculator::parallel

(

)

const

References parallel_.

Referenced by PointMutationCalculator().

protocols::moves::MoverOP protocols::design_opt::PointMutationCalculator::relax_mover

(

)

const

References relax_mover_.

Referenced by PointMutationCalculator().

void protocols::design_opt::PointMutationCalculator::relax_mover

(

protocols::moves::MoverOP

relax_mover

)

References relax_mover_.

void protocols::design_opt::PointMutationCalculator::rtmin

(

bool const

r

)

References rtmin_.

bool protocols::design_opt::PointMutationCalculator::rtmin

(

)

const

References rtmin_.

Referenced by PointMutationCalculator().

vector1< std::string > protocols::design_opt::PointMutationCalculator::sample_types

(

)

const

References sample_types_.

Referenced by PointMutationCalculator(), and sample_types().

void protocols::design_opt::PointMutationCalculator::sample_types

(

utility::vector1< std::string > const &

sample_types

)

References sample_types(), and sample_types_.

core::scoring::ScoreFunctionOP protocols::design_opt::PointMutationCalculator::scorefxn

(

)

const

References scorefxn_.

Referenced by PointMutationCalculator(), and scorefxn().

void protocols::design_opt::PointMutationCalculator::scorefxn

(

core::scoring::ScoreFunctionOP

scorefxn

)

References scorefxn(), and scorefxn_.

void protocols::design_opt::PointMutationCalculator::set_design_shell

(

core::Real

dz_shell

)

References design_shell_.

void protocols::design_opt::PointMutationCalculator::set_repack_shell

(

core::Real

rp_shell

)

References repack_shell_.

core::pack::task::TaskFactoryOP protocols::design_opt::PointMutationCalculator::task_factory

(

)

const

References task_factory_.

Referenced by PointMutationCalculator(), and task_factory().

void protocols::design_opt::PointMutationCalculator::task_factory

(

core::pack::task::TaskFactoryOP

task_factory

)

References task_factory(), and task_factory_.

Member Data Documentation

core::Real protocols::design_opt::PointMutationCalculator::design_shell_

private

Referenced by PointMutationCalculator(), and set_design_shell().

bool protocols::design_opt::PointMutationCalculator::dump_pdb_

private

Referenced by dump_pdb(), and PointMutationCalculator().

utility::vector1< protocols::filters::FilterOP > protocols::design_opt::PointMutationCalculator::filters_

private

Referenced by filters(), and PointMutationCalculator().

bool protocols::design_opt::PointMutationCalculator::parallel_

private

Referenced by parallel(), and PointMutationCalculator().

protocols::moves::MoverOP protocols::design_opt::PointMutationCalculator::relax_mover_

private

Referenced by PointMutationCalculator(), and relax_mover().

core::Real protocols::design_opt::PointMutationCalculator::repack_shell_

private

Referenced by PointMutationCalculator(), and set_repack_shell().

bool protocols::design_opt::PointMutationCalculator::rtmin_

private

Referenced by PointMutationCalculator(), and rtmin().

utility::vector1< std::string > protocols::design_opt::PointMutationCalculator::sample_types_

private

Referenced by PointMutationCalculator(), and sample_types().

core::scoring::ScoreFunctionOP protocols::design_opt::PointMutationCalculator::scorefxn_

private

Referenced by PointMutationCalculator(), and scorefxn().

core::pack::task::TaskFactoryOP protocols::design_opt::PointMutationCalculator::task_factory_

private

Referenced by PointMutationCalculator(), and task_factory().

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

• src/protocols/design_opt/PointMutationCalculator.hh
• src/protocols/design_opt/PointMutationCalculator.cc