PhProtocol Class Reference

Inheritance diagram for PhProtocol:

Public Member Functions
	PhProtocol ()
virtual	~PhProtocol ()
void	set_default ()
void	init_options ()
void	set_file_name (std::string pdb_file_name)
void	set_res_no (utility::vector1< core::Real > pdb_res_nos)
void	set_chain_no (std::string 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 pdbname)
void	relax_pose (core::pose::Pose &pose, std::string 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)
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

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::PhProtocol ( )

inline

References init_options().

virtual PhProtocol::~PhProtocol ( )

inlinevirtual

Member Function Documentation

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

inlinevirtual

References basic::options::OptionKeys::chemical::chemical, final_res_list_, finalize_res_list(), init_options(), ipka_, method_code_, old_pose_, pdb_file_name_, pH_neighbor_pack_, pH_prepack_, pH_relax_, pka_value_, app.surface_docking.surface_docking::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 src.protocols.jd2.RosettaScriptWrapper::apply_to_failure().

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

inline

References final_res_list_, pdb_chain_no_, pdb_res_nos_, pka_all_, and basic::options::OptionKeys::frags::scoring::scoring.

Referenced by apply().

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

inlinevirtual

std::string PhProtocol::get_name ( ) const

inline

void PhProtocol::init_options ( )

inline

References option, options, 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, basic::options::OptionKeys::in::file::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().

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

inline

References pyrosetta::get_score_function, test.T200_Scoring::ii, app.surface_docking.surface_docking::pose, basic::options::OptionKeys::frags::scoring::scoring, and TR().

Referenced by apply().

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

inline

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

virtual bool PhProtocol::reinitialize_for_each_job ( ) const

inlinevirtual

virtual bool PhProtocol::reinitialize_for_new_input ( ) const

inlinevirtual

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

inline

References pyrosetta::get_score_function, app.surface_docking.surface_docking::pose, basic::options::OptionKeys::frags::scoring::scoring, and TR().

Referenced by apply().

void PhProtocol::set_chain_no ( std::string  pdb_chain_no )

inline

References pdb_chain_no_.

Referenced by init_options().

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().

void PhProtocol::set_file_name ( std::string  pdb_file_name )

inline

References pdb_file_name_.

Referenced by init_options().

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().

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().

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().

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().

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().

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

inline

References pdb_res_nos_.

Referenced by init_options().

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().

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 basic::options::OptionKeys::chemical::chemical, curr_pose_, distance(), pyrosetta::get_score_function, test.T200_Scoring::ii, neighbor_count_, old_pose_, test.Workshop6test::pack_mover, pH_neighbor_pack_, pka_rad_, pka_value_, app.surface_docking.surface_docking::pose, refine_stage_, rotamer_prot_stats_, test.T200_Scoring::rsd1, test.T200_Scoring::rsd2, shift_pH_, app.delta_score_per_mutation::task, titration_successful_, and TR().

Referenced by apply().

Member Data Documentation

core::pose::Pose PhProtocol::curr_pose_

private

Referenced by titrate_pH().

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

private

Referenced by apply(), and finalize_res_list().

core::Real PhProtocol::ipka_

private

Referenced by apply(), and set_default().

std::string PhProtocol::method_code_

private

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

core::Size PhProtocol::neighbor_count_

private

Referenced by set_default(), and titrate_pH().

core::pose::Pose PhProtocol::old_pose_

private

Referenced by apply(), and titrate_pH().

std::string PhProtocol::pdb_chain_no_

private

Referenced by finalize_res_list(), and set_chain_no().

std::string PhProtocol::pdb_file_name_

private

Referenced by apply(), and set_file_name().

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

private

Referenced by finalize_res_list(), and set_res_no().

bool PhProtocol::pH_neighbor_pack_

private

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

bool PhProtocol::pH_prepack_

private

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

bool PhProtocol::pH_relax_

private

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

bool PhProtocol::pka_all_

private

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

core::Real PhProtocol::pka_rad_

private

Referenced by set_pka_rad(), and titrate_pH().

core::Real PhProtocol::pka_value_

private

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

bool PhProtocol::refine_stage_

private

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

bool PhProtocol::rotamer_prot_stats_

private

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

core::Real PhProtocol::shift_pH_

private

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

bool PhProtocol::titration_successful_

private

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

---

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

• src/apps/public/pH_protocol.cc