HBondReporter Class Reference

Inheritance diagram for HBondReporter:

Public Member Functions
	HBondReporter ()
virtual	~HBondReporter ()
void	load_job_data (Pose &pose)
string	pose_name (Pose &pose)
void	get_aa_counts (Pose &pose)
Real	bfactor (Pose &pose, Size resNum, Size atm, bool is_backbone)
void	decoyify (Pose &pose)
virtual void	apply (Pose &pose)
	HBondReporter ()
	~HBondReporter () override=default
std::string	get_name () const override
void	load_job_data (Pose &pose)
	What is this for? More...
std::string	pose_name (pose::Pose &pose)
	Returns a string representing the name of this pose. Uses the pdb_info object or the job distributor tag if no pdb_info object exists. More...
Real	bfactor (pose::Pose &pose, Size resNum, Size atm, bool is_backbone)
	Runs a "simple multi relax" protocol on the whole pose, or if the relevant chains flag was used on just the relevant chains. But only if the relax flag was specified. I want this executable/mover to only print Hbond info. If a user wants to relax their structure or do st else to it, they need to run that protocol first and then use this one to get Hbond info. More...
void	apply (pose::Pose &pose) override

Private Attributes
bool	allowNonProtein_ { true }
core::scoring::ScoreFunctionOP	scfxn
std::string	relevant_chains_
HBondDatabaseCOP	hb_database_

Constructor & Destructor Documentation

HBondReporter() [1/2]

HBondReporter::HBondReporter ( )

inline

~HBondReporter() [1/2]

virtual HBondReporter::~HBondReporter ( )

inlinevirtual

HBondReporter() [2/2]

HBondReporter::HBondReporter ( )

inline

~HBondReporter() [2/2]

HBondReporter::~HBondReporter ( )

overridedefault

Member Function Documentation

apply() [1/2]

virtual void HBondReporter::apply ( Pose &  pose )

inlinevirtual

References job_manager::app, test.T005_Bindings::base, kic_runner::database, basic::options::OptionKeys::in::file::dssp, oop_conformations::energy, val2thr::fout, create_a3b_hbs::i, basic::options::option, erraser_single_res_analysis::out, bin_torsions::output, output_filename, beta_nonlocal::pose, bur_nodon_tyr::probe_radius, basic::options::OptionKeys::abinitio::relax, rna_rosetta_ready_set::start_time, utility::file::FileName::to_local_name(), TR, basic::options::OptionKeys::inout::dbms::user, value, basic::options::OptionKeys::sc::weight, numeric::xyzVector< T >::x(), numeric::xyzVector< T >::y(), and numeric::xyzVector< T >::z().

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

apply() [2/2]

void HBondReporter::apply ( pose::Pose &  pose )

inlineoverride

References utility::io::oc::cout, basic::options::OptionKeys::in::file::dssp, oop_conformations::energy, ObjexxFCL::format::F(), create_a3b_hbs::i, test.T110_numeric::I, beta_nonlocal::pose, bur_nodon_tyr::probe_radius, TR, and basic::options::OptionKeys::sc::weight.

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

bfactor() [1/2]

Real HBondReporter::bfactor ( Pose &  pose, Size  resNum, Size  atm, bool  is_backbone  )

inline

References create_a3b_hbs::i, max(), natoms(), and beta_nonlocal::pose.

bfactor() [2/2]

Real HBondReporter::bfactor ( pose::Pose &  pose, Size  resNum, Size  atm, bool  is_backbone  )

inline

Runs a "simple multi relax" protocol on the whole pose, or if the relevant chains flag was used on just the relevant chains. But only if the relax flag was specified. I want this executable/mover to only print Hbond info. If a user wants to relax their structure or do st else to it, they need to run that protocol first and then use this one to get Hbond info.

Given a pose and a residue position, returns the bfactor for that residue. Why do we care about bfactors?

References create_a3b_hbs::ii, max(), natoms(), and beta_nonlocal::pose.

decoyify()

void HBondReporter::decoyify ( Pose &  pose )

inline

References create_a3b_hbs::j, beta_nonlocal::mm, beta_nonlocal::pose, basic::options::OptionKeys::abinitio::relax, and TR.

get_aa_counts()

void HBondReporter::get_aa_counts ( Pose &  pose )

inline

References create_a3b_hbs::i, beta_nonlocal::pose, and TR.

get_name()

std::string HBondReporter::get_name ( ) const

inlineoverride

load_job_data() [1/2]

void HBondReporter::load_job_data ( Pose &  pose )

inline

References chains, basic::Tracer::Error, getline(), ObjexxFCL::is_any_of(), line, solution_counts::lines, basic::options::option, beta_nonlocal::pose, binder::split(), utility::file::FileName::to_local_name(), and TR.

load_job_data() [2/2]

void HBondReporter::load_job_data ( Pose &  pose )

inline

What is this for?

References chains, getline(), ObjexxFCL::is_any_of(), line, solution_counts::lines, basic::options::option, beta_nonlocal::pose, binder::split(), utility::file::FileName::to_local_name(), TR, and basic::options::OptionKeys::inout::dbms::user.

pose_name() [1/2]

string HBondReporter::pose_name ( Pose &  pose )

inline

References name, beta_nonlocal::pose, and str().

pose_name() [2/2]

std::string HBondReporter::pose_name ( pose::Pose &  pose )

inline

Returns a string representing the name of this pose. Uses the pdb_info object or the job distributor tag if no pdb_info object exists.

References beta_nonlocal::pose, and str().

Member Data Documentation

allowNonProtein_

bool HBondReporter::allowNonProtein_ { true }

private

hb_database_

HBondDatabaseCOP HBondReporter::hb_database_

private

relevant_chains_

std::string HBondReporter::relevant_chains_

private

scfxn

core::scoring::ScoreFunctionOP HBondReporter::scfxn

private

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

• src/apps/pilot/momeara/report_hbonds.cc
• src/apps/public/analysis/report_hbonds_for_plugin.cc