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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 ()
 
 ~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::PhProtocol ( )
inline

References init_options().

PhProtocol::~PhProtocol ( )
overridedefault

Member Function Documentation

void PhProtocol::apply ( core::pose::Pose pose)
inlineoverride
void PhProtocol::finalize_res_list ( core::pose::Pose pose)
inline
protocols::moves::MoverOP PhProtocol::fresh_instance ( ) const
inlineoverride
std::string PhProtocol::get_name ( ) const
inlineoverride
void PhProtocol::init_options ( )
inline
void PhProtocol::prepack_pose ( core::pose::Pose pose,
std::string const &  pdbname 
)
inline
void PhProtocol::print_hbonds ( core::pose::Pose pose)
inline
bool PhProtocol::reinitialize_for_each_job ( ) const
inlineoverride
bool PhProtocol::reinitialize_for_new_input ( ) const
inlineoverride
void PhProtocol::relax_pose ( core::pose::Pose pose,
std::string const &  pdbname 
)
inline
void PhProtocol::set_chain_no ( std::string const &  pdb_chain_no)
inline

References pdb_chain_no_.

Referenced by init_options().

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

References pdb_file_name_.

Referenced by init_options().

void PhProtocol::set_pH_neighbor_pack ( bool  pH_neighbor_pack)
inline
void PhProtocol::set_pH_prepack ( bool  pH_prepack)
inline
void PhProtocol::set_pH_relax ( bool  pH_relax)
inline
void PhProtocol::set_pka_all ( bool  pka_all)
inline
void PhProtocol::set_pka_rad ( core::Real  pka_rad)
inline
void PhProtocol::set_res_no ( utility::vector1< core::Real > const &  pdb_res_nos)
inline

References pdb_res_nos_.

Referenced by init_options().

void PhProtocol::set_rotamer_prot_stats ( bool  rotamer_prot_stats)
inline
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

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
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
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
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
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: