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protocols::design_opt::PointMutationCalculator Class Reference

#include <PointMutationCalculator.hh>

Inheritance diagram for protocols::design_opt::PointMutationCalculator:
Inheritance graph
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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

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 
)
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 
)
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 
)
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
bool protocols::design_opt::PointMutationCalculator::dump_pdb_
private
utility::vector1< protocols::filters::FilterOP > protocols::design_opt::PointMutationCalculator::filters_
private

Referenced by filters(), and PointMutationCalculator().

bool protocols::design_opt::PointMutationCalculator::parallel_
private
protocols::moves::MoverOP protocols::design_opt::PointMutationCalculator::relax_mover_
private
core::Real protocols::design_opt::PointMutationCalculator::repack_shell_
private
bool protocols::design_opt::PointMutationCalculator::rtmin_
private

Referenced by PointMutationCalculator(), and rtmin().

utility::vector1< std::string > protocols::design_opt::PointMutationCalculator::sample_types_
private
core::scoring::ScoreFunctionOP protocols::design_opt::PointMutationCalculator::scorefxn_
private
core::pack::task::TaskFactoryOP protocols::design_opt::PointMutationCalculator::task_factory_
private

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