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Public Member Functions | Private Attributes | List of all members
PhProtocol Class Reference
Inheritance diagram for PhProtocol:
Inheritance graph
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Public Member Functions

 PhProtocol ()
 
virtual ~PhProtocol ()
 
virtual void apply (core::pose::Pose &pose)
 
std::string get_name () const
 
virtual protocols::moves::MoverOP fresh_instance () const
 
virtual bool reinitialize_for_each_job () const
 
virtual bool reinitialize_for_new_input () const
 
 PhProtocol ()
 
 ~PhProtocol () override=default
 
void set_default ()
 
void init_options ()
 
void set_file_name (std::string const &pdb_file_name)
 
void set_res_no (utility::vector1< core::Real > const &pdb_res_nos)
 
void set_chain_no (std::string const &pdb_chain_no)
 
void set_pka_all (bool pka_all)
 
void set_pH_prepack (bool pH_prepack)
 
void set_pH_relax (bool pH_relax)
 
void set_pH_neighbor_pack (bool pH_neighbor_pack)
 
void set_pka_rad (core::Real pka_rad)
 
void set_rotamer_prot_stats (bool rotamer_prot_stats)
 
void print_hbonds (core::pose::Pose &pose)
 
void prepack_pose (core::pose::Pose &pose, std::string const &pdbname)
 
void relax_pose (core::pose::Pose &pose, std::string const &pdbname)
 
void titrate_pH (core::pose::Pose &pose, core::Size res_no, core::Real start_pH, core::Real stop_pH, core::Real step_size)
 
void finalize_res_list (core::pose::Pose &pose)
 
void apply (core::pose::Pose &pose) override
 
std::string get_name () const override
 
protocols::moves::MoverOP fresh_instance () const override
 
bool reinitialize_for_each_job () const override
 
bool reinitialize_for_new_input () const override
 

Private Attributes

core::pose::Pose old_pose_
 
core::pose::Pose curr_pose_
 
bool pka_all_
 
bool refine_stage_
 
bool pH_prepack_
 
bool pH_relax_
 
bool pH_neighbor_pack_
 
bool rotamer_prot_stats_
 
bool titration_successful_
 
core::Real shift_pH_
 
core::Real pka_value_
 
core::Real ipka_
 
core::Real pka_rad_
 
std::string pdb_file_name_
 
utility::vector1< core::Real > pdb_res_nos_
 
utility::vector1< core::Size > final_res_list_
 
std::string pdb_chain_no_
 
std::string method_code_
 
core::Size neighbor_count_
 

Constructor & Destructor Documentation

◆ PhProtocol() [1/2]

PhProtocol::PhProtocol ( )
inline

Referenced by fresh_instance().

◆ ~PhProtocol() [1/2]

virtual PhProtocol::~PhProtocol ( )
inlinevirtual

◆ PhProtocol() [2/2]

PhProtocol::PhProtocol ( )
inline

References init_options().

◆ ~PhProtocol() [2/2]

PhProtocol::~PhProtocol ( )
overridedefault

Member Function Documentation

◆ apply() [1/2]

virtual void PhProtocol::apply ( core::pose::Pose &  pose)
inlinevirtual

References utility::io::oc::cout, enumerate_junctions::default, create_a3b_hbs::ii, option, test.Workshop6test::pack_mover, basic::options::OptionKeys::pH::calc_pka::pka_for_chainno, basic::options::OptionKeys::pH::calc_pka::pka_rad, beta_nonlocal::pose, erraser_analysis::res1, erraser_analysis::res2, docking::s, beta_nonlocal::score_fxn, vancomycin::task, and TR.

Referenced by pyrosetta.distributed.tasks.rosetta_scripts.BaseRosettaScriptsTask::execute().

◆ apply() [2/2]

void PhProtocol::apply ( core::pose::Pose &  pose)
inlineoverride

References enumerate_junctions::default, final_res_list_, finalize_res_list(), init_options(), ipka_, method_code_, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, old_pose_, pdb_file_name_, pH_neighbor_pack_, pH_prepack_, pH_relax_, pka_value_, beta_nonlocal::pose, prepack_pose(), refine_stage_, relax_pose(), rotamer_prot_stats_, basic::options::OptionKeys::frags::scoring::scoring, shift_pH_, titrate_pH(), titration_successful_, and TR.

Referenced by pyrosetta.distributed.tasks.rosetta_scripts.BaseRosettaScriptsTask::execute().

◆ finalize_res_list()

void PhProtocol::finalize_res_list ( core::pose::Pose &  pose)
inline

References final_res_list_, create_a3b_hbs::i, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, pdb_chain_no_, pdb_res_nos_, pka_all_, beta_nonlocal::pose, and basic::options::OptionKeys::frags::scoring::scoring.

Referenced by apply().

◆ fresh_instance() [1/2]

virtual protocols::moves::MoverOP PhProtocol::fresh_instance ( ) const
inlinevirtual

References PhProtocol().

◆ fresh_instance() [2/2]

protocols::moves::MoverOP PhProtocol::fresh_instance ( ) const
inlineoverride

◆ get_name() [1/2]

std::string PhProtocol::get_name ( ) const
inline

◆ get_name() [2/2]

std::string PhProtocol::get_name ( ) const
inlineoverride

◆ init_options()

void PhProtocol::init_options ( )
inline

References option, basic::options::OptionKeys::pH::calc_pka::pH_neighbor_pack, basic::options::OptionKeys::pH::calc_pka::pH_prepack, basic::options::OptionKeys::pH::calc_pka::pH_relax, basic::options::OptionKeys::pH::calc_pka::pka_all, basic::options::OptionKeys::pH::calc_pka::pka_for_chainno, basic::options::OptionKeys::pH::calc_pka::pka_for_resnos, basic::options::OptionKeys::pH::calc_pka::pka_rad, basic::options::OptionKeys::pH::calc_pka::rotamer_prot_stats, docking::s, set_chain_no(), set_default(), set_file_name(), set_pH_neighbor_pack(), set_pH_prepack(), set_pH_relax(), set_pka_all(), set_pka_rad(), set_res_no(), set_rotamer_prot_stats(), and basic::options::OptionKeys::inout::dbms::user.

Referenced by apply(), and PhProtocol().

◆ prepack_pose()

void PhProtocol::prepack_pose ( core::pose::Pose &  pose,
std::string const &  pdbname 
)
inline

References create_a3b_hbs::ii, predPRE::pdbname, beta_nonlocal::pose, beta_nonlocal::score_fxn, basic::options::OptionKeys::frags::scoring::scoring, and TR.

Referenced by apply().

◆ print_hbonds()

void PhProtocol::print_hbonds ( core::pose::Pose &  pose)
inline

References utility::io::oc::cout, beta_nonlocal::pose, and basic::options::OptionKeys::frags::scoring::scoring.

◆ reinitialize_for_each_job() [1/2]

virtual bool PhProtocol::reinitialize_for_each_job ( ) const
inlinevirtual

◆ reinitialize_for_each_job() [2/2]

bool PhProtocol::reinitialize_for_each_job ( ) const
inlineoverride

◆ reinitialize_for_new_input() [1/2]

virtual bool PhProtocol::reinitialize_for_new_input ( ) const
inlinevirtual

◆ reinitialize_for_new_input() [2/2]

bool PhProtocol::reinitialize_for_new_input ( ) const
inlineoverride

◆ relax_pose()

void PhProtocol::relax_pose ( core::pose::Pose &  pose,
std::string const &  pdbname 
)
inline

References predPRE::pdbname, beta_nonlocal::pose, beta_nonlocal::score_fxn, basic::options::OptionKeys::frags::scoring::scoring, and TR.

Referenced by apply().

◆ set_chain_no()

void PhProtocol::set_chain_no ( std::string const &  pdb_chain_no)
inline

References pdb_chain_no_.

Referenced by init_options().

◆ set_default()

void PhProtocol::set_default ( )
inline

References ipka_, method_code_, neighbor_count_, pH_neighbor_pack_, pH_prepack_, pH_relax_, pka_all_, pka_value_, refine_stage_, rotamer_prot_stats_, shift_pH_, and titration_successful_.

Referenced by init_options().

◆ set_file_name()

void PhProtocol::set_file_name ( std::string const &  pdb_file_name)
inline

References pdb_file_name_.

Referenced by init_options().

◆ set_pH_neighbor_pack()

void PhProtocol::set_pH_neighbor_pack ( bool  pH_neighbor_pack)
inline

References method_code_, basic::options::OptionKeys::pH::calc_pka::pH_neighbor_pack, and pH_neighbor_pack_.

Referenced by init_options().

◆ set_pH_prepack()

void PhProtocol::set_pH_prepack ( bool  pH_prepack)
inline

References method_code_, basic::options::OptionKeys::pH::calc_pka::pH_prepack, and pH_prepack_.

Referenced by init_options().

◆ set_pH_relax()

void PhProtocol::set_pH_relax ( bool  pH_relax)
inline

References basic::options::OptionKeys::pH::calc_pka::pH_relax, and pH_relax_.

Referenced by init_options().

◆ set_pka_all()

void PhProtocol::set_pka_all ( bool  pka_all)
inline

References basic::options::OptionKeys::pH::calc_pka::pka_all, and pka_all_.

Referenced by init_options().

◆ set_pka_rad()

void PhProtocol::set_pka_rad ( core::Real  pka_rad)
inline

References basic::options::OptionKeys::pH::calc_pka::pka_rad, and pka_rad_.

Referenced by init_options().

◆ set_res_no()

void PhProtocol::set_res_no ( utility::vector1< core::Real > const &  pdb_res_nos)
inline

References pdb_res_nos_.

Referenced by init_options().

◆ set_rotamer_prot_stats()

void PhProtocol::set_rotamer_prot_stats ( bool  rotamer_prot_stats)
inline

References basic::options::OptionKeys::pH::calc_pka::rotamer_prot_stats, and rotamer_prot_stats_.

Referenced by init_options().

◆ titrate_pH()

void PhProtocol::titrate_pH ( core::pose::Pose &  pose,
core::Size  res_no,
core::Real  start_pH,
core::Real  stop_pH,
core::Real  step_size 
)
inline

References curr_pose_, build_jacobian::distance, create_a3b_hbs::ii, beta_nonlocal::jj, neighbor_count_, old_pose_, test.Workshop6test::pack_mover, pH_neighbor_pack_, pka_rad_, pka_value_, beta_nonlocal::pose, refine_stage_, erraser_analysis::res1, erraser_analysis::res2, rotamer_prot_stats_, test.T200_Scoring::rsd1, test.T200_Scoring::rsd2, beta_nonlocal::score_fxn, shift_pH_, vancomycin::task, titration_successful_, and TR.

Referenced by apply().

Member Data Documentation

◆ curr_pose_

core::pose::Pose PhProtocol::curr_pose_
private

Referenced by titrate_pH().

◆ final_res_list_

utility::vector1< core::Size > PhProtocol::final_res_list_
private

Referenced by apply(), and finalize_res_list().

◆ ipka_

core::Real PhProtocol::ipka_
private

Referenced by apply(), and set_default().

◆ method_code_

std::string PhProtocol::method_code_
private

Referenced by apply(), set_default(), set_pH_neighbor_pack(), and set_pH_prepack().

◆ neighbor_count_

core::Size PhProtocol::neighbor_count_
private

Referenced by set_default(), and titrate_pH().

◆ old_pose_

core::pose::Pose PhProtocol::old_pose_
private

Referenced by apply(), and titrate_pH().

◆ pdb_chain_no_

std::string PhProtocol::pdb_chain_no_
private

Referenced by finalize_res_list(), and set_chain_no().

◆ pdb_file_name_

std::string PhProtocol::pdb_file_name_
private

Referenced by apply(), and set_file_name().

◆ pdb_res_nos_

utility::vector1< core::Real > PhProtocol::pdb_res_nos_
private

Referenced by finalize_res_list(), and set_res_no().

◆ pH_neighbor_pack_

bool PhProtocol::pH_neighbor_pack_
private

Referenced by apply(), set_default(), set_pH_neighbor_pack(), and titrate_pH().

◆ pH_prepack_

bool PhProtocol::pH_prepack_
private

Referenced by apply(), set_default(), and set_pH_prepack().

◆ pH_relax_

bool PhProtocol::pH_relax_
private

Referenced by apply(), set_default(), and set_pH_relax().

◆ pka_all_

bool PhProtocol::pka_all_
private

Referenced by finalize_res_list(), set_default(), and set_pka_all().

◆ pka_rad_

core::Real PhProtocol::pka_rad_
private

Referenced by set_pka_rad(), and titrate_pH().

◆ pka_value_

core::Real PhProtocol::pka_value_
private

Referenced by apply(), set_default(), and titrate_pH().

◆ refine_stage_

bool PhProtocol::refine_stage_
private

Referenced by apply(), set_default(), and titrate_pH().

◆ rotamer_prot_stats_

bool PhProtocol::rotamer_prot_stats_
private

Referenced by apply(), set_default(), set_rotamer_prot_stats(), and titrate_pH().

◆ shift_pH_

core::Real PhProtocol::shift_pH_
private

Referenced by apply(), set_default(), and titrate_pH().

◆ titration_successful_

bool PhProtocol::titration_successful_
private

Referenced by apply(), set_default(), and titrate_pH().

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