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protocols::matdes::MatDesPointMutationCalculator Class Reference

#include <MatDesPointMutationCalculator.hh>

Inheritance diagram for protocols::matdes::MatDesPointMutationCalculator:
Inheritance graph
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Public Types

typedef core::pose::Pose Pose
 

Public Member Functions

 MatDesPointMutationCalculator ()
 default ctor More...
 
 MatDesPointMutationCalculator (core::pack::task::TaskFactoryOP task_factory, core::scoring::ScoreFunctionOP scorefxn, protocols::moves::MoverOP relax_mover, utility::vector1< protocols::filters::FilterOP > filters, utility::vector1< std::pair< std::string, core::Real > > filter_thresholds, utility::vector1< protocols::simple_filters::TaskAwareScoreTypeFilterOP > set_task_for_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, bool force_natro=false)
 
 MatDesPointMutationCalculator (core::pack::task::TaskFactoryOP task_factory, core::scoring::ScoreFunctionOP scorefxn, protocols::moves::MoverOP relax_mover, protocols::filters::FilterOP filter, std::pair< std::string, core::Real > filter_threshold, protocols::simple_filters::TaskAwareScoreTypeFilterOP set_task_for_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, bool force_natro=false)
 
 ~MatDesPointMutationCalculator () 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, bool always_eval)
 
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::matdes::MatDesPointMutationCalculatorOP 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)
 
utility::vector1< std::pair< std::string, core::Real > > filter_thresholds () const
 
void filter_thresholds (utility::vector1< std::pair< std::string, core::Real > > filter_thresholds)
 
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)
 
utility::vector1< protocols::simple_filters::TaskAwareScoreTypeFilterOP > set_task_for_filters () const
 
void set_task_for_filters (utility::vector1< protocols::simple_filters::TaskAwareScoreTypeFilterOP > set_task_for_filters)
 
void force_natro (bool const force_natro)
 
bool force_natro () const
 
void stored_task_names (utility::vector1< std::string > stored_task_names)
 
utility::vector1< std::string > stored_task_names () const
 
void new_tasks (utility::vector1< core::pack::task::PackerTaskOP > new_tasks)
 
utility::vector1< core::pack::task::PackerTaskOP > new_tasks () const
 
core::pose::PoseOP reference_pose () const
 
void reference_pose (core::pose::PoseOP const reference_pose)
 

Private Attributes

core::pack::task::TaskFactoryOP task_factory_
 
core::scoring::ScoreFunctionOP scorefxn_
 
utility::vector1< protocols::filters::FilterOP > filters_
 
utility::vector1< std::pair< std::string, core::Real > > filter_thresholds_
 
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_
 
utility::vector1< protocols::simple_filters::TaskAwareScoreTypeFilterOP > set_task_for_filters_
 
bool force_natro_
 
utility::vector1< std::string > stored_task_names_
 
utility::vector1< core::pack::task::PackerTaskOP > new_tasks_
 
core::pose::PoseOP reference_pose_
 

Member Typedef Documentation

◆ Pose

typedef core::pose::Pose protocols::matdes::MatDesPointMutationCalculator::Pose

Constructor & Destructor Documentation

◆ MatDesPointMutationCalculator() [1/3]

protocols::matdes::MatDesPointMutationCalculator::MatDesPointMutationCalculator ( )

default ctor

◆ MatDesPointMutationCalculator() [2/3]

protocols::matdes::MatDesPointMutationCalculator::MatDesPointMutationCalculator ( core::pack::task::TaskFactoryOP  task_factory,
core::scoring::ScoreFunctionOP  scorefxn,
protocols::moves::MoverOP  relax_mover,
utility::vector1< protocols::filters::FilterOP >  filters,
utility::vector1< std::pair< std::string, core::Real > >  filter_thresholds,
utility::vector1< protocols::simple_filters::TaskAwareScoreTypeFilterOP >  set_task_for_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,
bool  force_natro = false 
)

◆ MatDesPointMutationCalculator() [3/3]

protocols::matdes::MatDesPointMutationCalculator::MatDesPointMutationCalculator ( core::pack::task::TaskFactoryOP  task_factory,
core::scoring::ScoreFunctionOP  scorefxn,
protocols::moves::MoverOP  relax_mover,
protocols::filters::FilterOP  filter,
std::pair< std::string, core::Real >  filter_threshold,
protocols::simple_filters::TaskAwareScoreTypeFilterOP  set_task_for_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,
bool  force_natro = false 
)

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

◆ ~MatDesPointMutationCalculator()

protocols::matdes::MatDesPointMutationCalculator::~MatDesPointMutationCalculator ( )
overridedefault

Member Function Documentation

◆ calc_point_mut_filters() [1/2]

void protocols::matdes::MatDesPointMutationCalculator::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 
)

◆ calc_point_mut_filters() [2/2]

void protocols::matdes::MatDesPointMutationCalculator::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 
)

◆ clone()

protocols::matdes::MatDesPointMutationCalculatorOP protocols::matdes::MatDesPointMutationCalculator::clone ( ) const

◆ dump_pdb() [1/2]

bool protocols::matdes::MatDesPointMutationCalculator::dump_pdb ( ) const

References dump_pdb_.

Referenced by dump_pdb(), and MatDesPointMutationCalculator().

◆ dump_pdb() [2/2]

void protocols::matdes::MatDesPointMutationCalculator::dump_pdb ( bool const  dump_pdb)

References dump_pdb(), and dump_pdb_.

◆ eval_filters()

void protocols::matdes::MatDesPointMutationCalculator::eval_filters ( core::pose::Pose &  pose,
bool &  filter_pass,
utility::vector1< core::Real > &  vals,
bool  always_eval 
)

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

◆ filter_thresholds() [1/2]

vector1< std::pair< std::string, core::Real > > protocols::matdes::MatDesPointMutationCalculator::filter_thresholds ( ) const

References filter_thresholds_.

Referenced by MatDesPointMutationCalculator().

◆ filter_thresholds() [2/2]

void protocols::matdes::MatDesPointMutationCalculator::filter_thresholds ( utility::vector1< std::pair< std::string, core::Real > >  filter_thresholds)

◆ filters() [1/2]

vector1< protocols::filters::FilterOP > protocols::matdes::MatDesPointMutationCalculator::filters ( ) const

References filters_.

Referenced by MatDesPointMutationCalculator().

◆ filters() [2/2]

void protocols::matdes::MatDesPointMutationCalculator::filters ( utility::vector1< protocols::filters::FilterOP >  filters)

◆ force_natro() [1/2]

bool protocols::matdes::MatDesPointMutationCalculator::force_natro ( ) const

References force_natro_.

Referenced by force_natro(), and MatDesPointMutationCalculator().

◆ force_natro() [2/2]

void protocols::matdes::MatDesPointMutationCalculator::force_natro ( bool const  force_natro)

References force_natro(), and force_natro_.

◆ mutate_and_relax() [1/2]

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

References core::pose::Pose::data(), core::pose::symmetry::is_symmetric(), core::pack::make_symmetric_PackerTask_by_truncation(), core::conformation::Residue::name3(), core::chemical::num_canonical_aas, core::pose::Pose::replace_residue(), core::pose::Pose::residue(), core::pose::Pose::size(), core::pose::datacache::CacheableDataType::STM_STORED_TASKS, and protocols::matdes::TR().

◆ mutate_and_relax() [2/2]

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

References core::pose::symmetry::is_symmetric(), core::conformation::Residue::name1(), core::chemical::num_canonical_aas, core::pose::Pose::residue(), and protocols::matdes::TR().

◆ new_tasks() [1/2]

utility::vector1< core::pack::task::PackerTaskOP > protocols::matdes::MatDesPointMutationCalculator::new_tasks ( ) const

References new_tasks_.

Referenced by new_tasks().

◆ new_tasks() [2/2]

void protocols::matdes::MatDesPointMutationCalculator::new_tasks ( utility::vector1< core::pack::task::PackerTaskOP >  new_tasks)

References new_tasks(), and new_tasks_.

◆ parallel() [1/2]

bool protocols::matdes::MatDesPointMutationCalculator::parallel ( ) const

References parallel_.

Referenced by MatDesPointMutationCalculator().

◆ parallel() [2/2]

void protocols::matdes::MatDesPointMutationCalculator::parallel ( bool const  r)

References parallel_.

◆ reference_pose() [1/2]

pose::PoseOP protocols::matdes::MatDesPointMutationCalculator::reference_pose ( ) const

References reference_pose_.

Referenced by reference_pose().

◆ reference_pose() [2/2]

void protocols::matdes::MatDesPointMutationCalculator::reference_pose ( core::pose::PoseOP const  reference_pose)

References reference_pose(), and reference_pose_.

◆ relax_mover() [1/2]

protocols::moves::MoverOP protocols::matdes::MatDesPointMutationCalculator::relax_mover ( ) const

References relax_mover_.

Referenced by MatDesPointMutationCalculator().

◆ relax_mover() [2/2]

void protocols::matdes::MatDesPointMutationCalculator::relax_mover ( protocols::moves::MoverOP  relax_mover)

References relax_mover_.

◆ rtmin() [1/2]

bool protocols::matdes::MatDesPointMutationCalculator::rtmin ( ) const

References rtmin_.

Referenced by MatDesPointMutationCalculator().

◆ rtmin() [2/2]

void protocols::matdes::MatDesPointMutationCalculator::rtmin ( bool const  r)

References rtmin_.

◆ sample_types() [1/2]

vector1< std::string > protocols::matdes::MatDesPointMutationCalculator::sample_types ( ) const

References sample_types_.

Referenced by MatDesPointMutationCalculator().

◆ sample_types() [2/2]

void protocols::matdes::MatDesPointMutationCalculator::sample_types ( utility::vector1< std::string > const &  sample_types)

◆ scorefxn() [1/2]

core::scoring::ScoreFunctionOP protocols::matdes::MatDesPointMutationCalculator::scorefxn ( ) const

References scorefxn_.

Referenced by MatDesPointMutationCalculator(), and scorefxn().

◆ scorefxn() [2/2]

void protocols::matdes::MatDesPointMutationCalculator::scorefxn ( core::scoring::ScoreFunctionOP  scorefxn)

References scorefxn(), and scorefxn_.

◆ set_design_shell()

void protocols::matdes::MatDesPointMutationCalculator::set_design_shell ( core::Real  dz_shell)

References design_shell_.

◆ set_repack_shell()

void protocols::matdes::MatDesPointMutationCalculator::set_repack_shell ( core::Real  rp_shell)

References repack_shell_.

◆ set_task_for_filters() [1/2]

vector1< protocols::simple_filters::TaskAwareScoreTypeFilterOP > protocols::matdes::MatDesPointMutationCalculator::set_task_for_filters ( ) const

References set_task_for_filters_.

Referenced by MatDesPointMutationCalculator().

◆ set_task_for_filters() [2/2]

void protocols::matdes::MatDesPointMutationCalculator::set_task_for_filters ( utility::vector1< protocols::simple_filters::TaskAwareScoreTypeFilterOP >  set_task_for_filters)

◆ stored_task_names() [1/2]

utility::vector1< std::string > protocols::matdes::MatDesPointMutationCalculator::stored_task_names ( ) const

References stored_task_names_.

Referenced by stored_task_names().

◆ stored_task_names() [2/2]

void protocols::matdes::MatDesPointMutationCalculator::stored_task_names ( utility::vector1< std::string >  stored_task_names)

References stored_task_names(), and stored_task_names_.

◆ task_factory() [1/2]

core::pack::task::TaskFactoryOP protocols::matdes::MatDesPointMutationCalculator::task_factory ( ) const

References task_factory_.

Referenced by MatDesPointMutationCalculator(), and task_factory().

◆ task_factory() [2/2]

void protocols::matdes::MatDesPointMutationCalculator::task_factory ( core::pack::task::TaskFactoryOP  task_factory)

References task_factory(), and task_factory_.

Member Data Documentation

◆ design_shell_

core::Real protocols::matdes::MatDesPointMutationCalculator::design_shell_
private

Referenced by MatDesPointMutationCalculator(), and set_design_shell().

◆ dump_pdb_

bool protocols::matdes::MatDesPointMutationCalculator::dump_pdb_
private

Referenced by dump_pdb(), and MatDesPointMutationCalculator().

◆ filter_thresholds_

utility::vector1< std::pair< std::string, core::Real > > protocols::matdes::MatDesPointMutationCalculator::filter_thresholds_
private

Referenced by filter_thresholds().

◆ filters_

utility::vector1< protocols::filters::FilterOP > protocols::matdes::MatDesPointMutationCalculator::filters_
private

Referenced by filters(), and MatDesPointMutationCalculator().

◆ force_natro_

bool protocols::matdes::MatDesPointMutationCalculator::force_natro_
private

Referenced by force_natro(), and MatDesPointMutationCalculator().

◆ new_tasks_

utility::vector1< core::pack::task::PackerTaskOP > protocols::matdes::MatDesPointMutationCalculator::new_tasks_
private

Referenced by new_tasks().

◆ parallel_

bool protocols::matdes::MatDesPointMutationCalculator::parallel_
private

Referenced by MatDesPointMutationCalculator(), and parallel().

◆ reference_pose_

core::pose::PoseOP protocols::matdes::MatDesPointMutationCalculator::reference_pose_
private

Referenced by reference_pose().

◆ relax_mover_

protocols::moves::MoverOP protocols::matdes::MatDesPointMutationCalculator::relax_mover_
private

Referenced by MatDesPointMutationCalculator(), and relax_mover().

◆ repack_shell_

core::Real protocols::matdes::MatDesPointMutationCalculator::repack_shell_
private

Referenced by MatDesPointMutationCalculator(), and set_repack_shell().

◆ rtmin_

bool protocols::matdes::MatDesPointMutationCalculator::rtmin_
private

Referenced by MatDesPointMutationCalculator(), and rtmin().

◆ sample_types_

utility::vector1< std::string > protocols::matdes::MatDesPointMutationCalculator::sample_types_
private

Referenced by MatDesPointMutationCalculator(), and sample_types().

◆ scorefxn_

core::scoring::ScoreFunctionOP protocols::matdes::MatDesPointMutationCalculator::scorefxn_
private

Referenced by MatDesPointMutationCalculator(), and scorefxn().

◆ set_task_for_filters_

utility::vector1< protocols::simple_filters::TaskAwareScoreTypeFilterOP > protocols::matdes::MatDesPointMutationCalculator::set_task_for_filters_
private

Referenced by set_task_for_filters().

◆ stored_task_names_

utility::vector1< std::string > protocols::matdes::MatDesPointMutationCalculator::stored_task_names_
private

Referenced by stored_task_names().

◆ task_factory_

core::pack::task::TaskFactoryOP protocols::matdes::MatDesPointMutationCalculator::task_factory_
private

Referenced by MatDesPointMutationCalculator(), and task_factory().

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