HbondZinc Class Reference

Inheritance diagram for HbondZinc:

Public Member Functions
	HbondZinc ()
virtual	~HbondZinc ()
virtual void	apply (core::pose::Pose &pose)
virtual void	find_zinc (core::pose::Pose &pose)
virtual void	graft_match (core::pose::Pose &pose)
virtual void	repack (core::pose::Pose &pose)
virtual void	constrain_zinc (core::pose::Pose &pose)
virtual void	find_neighbors (core::pose::Pose &pose)
virtual void	build_rotamers (core::pose::Pose &pose)
virtual void	hbond_constraint (core::pose::Pose &pose, Size hbond_res, Size aa_index, Size primary_shell_index, Size krot)
virtual std::string	get_name () const
	HbondZinc ()
virtual	~HbondZinc ()
virtual void	apply (core::pose::Pose &pose)
virtual void	find_zinc (core::pose::Pose &pose)
virtual void	graft_match (core::pose::Pose &pose)
virtual void	repack (core::pose::Pose &pose)
virtual void	find_neighbors (core::pose::Pose &pose)
virtual void	build_rotamers (core::pose::Pose &pose)
virtual std::string	get_name () const
	HbondZinc ()
virtual	~HbondZinc ()
virtual void	apply (core::pose::Pose &pose)
virtual void	find_zinc (core::pose::Pose &pose)
virtual void	graft_match (core::pose::Pose &pose)
virtual void	repack (core::pose::Pose &pose)
virtual void	find_neighbors (core::pose::Pose &pose)
virtual void	build_rotamers (core::pose::Pose &pose)
virtual std::string	get_name () const
	HbondZinc ()
virtual	~HbondZinc ()
virtual void	apply (core::pose::Pose &pose)
virtual void	find_zinc (core::pose::Pose &pose)
virtual void	graft_match (core::pose::Pose &pose)
virtual void	repack (core::pose::Pose &pose)
virtual void	constrain_zinc (core::pose::Pose &pose)
virtual void	find_neighbors (core::pose::Pose &pose)
virtual void	build_rotamers (core::pose::Pose &pose)
virtual void	hbond_constraint (core::pose::Pose &pose, Size hbond_res, Size aa_index, Size primary_shell_index, Size krot)
virtual std::string	get_name () const

Private Attributes
core::pose::Pose	starting_pose_
utility::vector1< protocols::metal_interface::MetalSiteResidueOP >	msr_
utility::vector1< utility::vector1< Size > >	primary_shell_neighbors_
Size	backsideO_His_
core::pose::Pose	match_pose_

Constructor & Destructor Documentation

HbondZinc() [1/4]

HbondZinc::HbondZinc ( )

inline

~HbondZinc() [1/4]

virtual HbondZinc::~HbondZinc ( )

inlinevirtual

HbondZinc() [2/4]

HbondZinc::HbondZinc ( )

inline

~HbondZinc() [2/4]

virtual HbondZinc::~HbondZinc ( )

inlinevirtual

HbondZinc() [3/4]

HbondZinc::HbondZinc ( )

inline

~HbondZinc() [3/4]

virtual HbondZinc::~HbondZinc ( )

inlinevirtual

HbondZinc() [4/4]

HbondZinc::HbondZinc ( )

inline

~HbondZinc() [4/4]

virtual HbondZinc::~HbondZinc ( )

inlinevirtual

Member Function Documentation

apply() [1/4]

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

inlinevirtual

References find_neighbors(), beta_nonlocal::pose, basic::options::OptionKeys::casp::repack, and TR.

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

apply() [2/4]

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

inlinevirtual

References find_neighbors(), beta_nonlocal::pose, basic::options::OptionKeys::casp::repack, and TR.

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

apply() [3/4]

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

inlinevirtual

References find_neighbors(), beta_nonlocal::pose, basic::options::OptionKeys::casp::repack, and TR.

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

apply() [4/4]

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

inlinevirtual

References find_neighbors(), beta_nonlocal::pose, basic::options::OptionKeys::casp::repack, and TR.

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

build_rotamers() [1/4]

virtual void HbondZinc::build_rotamers ( core::pose::Pose &  pose )

inlinevirtual

References create_a3b_hbs::i, create_a3b_hbs::j, beta_nonlocal::pose, res, oop_conformations::scorefxn, test.Workshop7test::starting_pose, vancomycin::task, and TR.

build_rotamers() [2/4]

virtual void HbondZinc::build_rotamers ( core::pose::Pose &  pose )

inlinevirtual

References create_a3b_hbs::i, create_a3b_hbs::j, localrmsd::output_name, beta_nonlocal::pose, res, oop_conformations::scorefxn, test.Workshop7test::starting_pose, vancomycin::task, and TR.

build_rotamers() [3/4]

virtual void HbondZinc::build_rotamers ( core::pose::Pose &  pose )

inlinevirtual

References create_a3b_hbs::i, create_a3b_hbs::j, localrmsd::output_name, beta_nonlocal::pose, res, oop_conformations::scorefxn, test.Workshop7test::starting_pose, and TR.

build_rotamers() [4/4]

virtual void HbondZinc::build_rotamers ( core::pose::Pose &  pose )

inlinevirtual

References create_a3b_hbs::i, create_a3b_hbs::j, beta_nonlocal::pose, res, oop_conformations::scorefxn, test.Workshop7test::starting_pose, vancomycin::task, and TR.

constrain_zinc() [1/2]

virtual void HbondZinc::constrain_zinc ( core::pose::Pose &  pose )

inlinevirtual

References beta_nonlocal::pose.

constrain_zinc() [2/2]

virtual void HbondZinc::constrain_zinc ( core::pose::Pose &  pose )

inlinevirtual

References basic::options::OptionKeys::constraints::constraints, numeric::conversions::degrees(), numeric::xyzVector< T >::distance(), vancomycin::min_mover, beta_nonlocal::mm, beta_nonlocal::pose, numeric::conversions::radians(), oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, and TR.

find_neighbors() [1/4]

virtual void HbondZinc::find_neighbors ( core::pose::Pose &  pose )

inlinevirtual

References end, create_a3b_hbs::i, create_a3b_hbs::j, beta_nonlocal::pose, TR, and basic::MetricValue< T >::value().

find_neighbors() [2/4]

virtual void HbondZinc::find_neighbors ( core::pose::Pose &  pose )

inlinevirtual

References end, create_a3b_hbs::i, create_a3b_hbs::j, beta_nonlocal::pose, TR, and basic::MetricValue< T >::value().

find_neighbors() [3/4]

virtual void HbondZinc::find_neighbors ( core::pose::Pose &  pose )

inlinevirtual

References end, create_a3b_hbs::i, beta_nonlocal::pose, TR, and basic::MetricValue< T >::value().

find_neighbors() [4/4]

virtual void HbondZinc::find_neighbors ( core::pose::Pose &  pose )

inlinevirtual

References end, create_a3b_hbs::i, create_a3b_hbs::j, beta_nonlocal::pose, TR, and basic::MetricValue< T >::value().

find_zinc() [1/4]

virtual void HbondZinc::find_zinc ( core::pose::Pose &  pose )

inlinevirtual

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

find_zinc() [2/4]

virtual void HbondZinc::find_zinc ( core::pose::Pose &  pose )

inlinevirtual

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

find_zinc() [3/4]

virtual void HbondZinc::find_zinc ( core::pose::Pose &  pose )

inlinevirtual

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

find_zinc() [4/4]

virtual void HbondZinc::find_zinc ( core::pose::Pose &  pose )

inlinevirtual

References create_a3b_hbs::i, test.T120_core::match_pose, and beta_nonlocal::pose.

get_name() [1/4]

virtual std::string HbondZinc::get_name ( ) const

inlinevirtual

get_name() [2/4]

virtual std::string HbondZinc::get_name ( ) const

inlinevirtual

get_name() [3/4]

virtual std::string HbondZinc::get_name ( ) const

inlinevirtual

get_name() [4/4]

virtual std::string HbondZinc::get_name ( ) const

inlinevirtual

graft_match() [1/4]

virtual void HbondZinc::graft_match ( core::pose::Pose &  pose )

inlinevirtual

References create_a3b_hbs::i, basic::options::option, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, scaffold_protein, TR, and value.

graft_match() [2/4]

virtual void HbondZinc::graft_match ( core::pose::Pose &  pose )

inlinevirtual

References create_a3b_hbs::i, basic::options::option, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, scaffold_protein, TR, and value.

graft_match() [3/4]

virtual void HbondZinc::graft_match ( core::pose::Pose &  pose )

inlinevirtual

References create_a3b_hbs::i, basic::options::option, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, scaffold_protein, TR, and value.

graft_match() [4/4]

virtual void HbondZinc::graft_match ( core::pose::Pose &  pose )

inlinevirtual

References create_a3b_hbs::i, basic::options::option, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, scaffold_protein, TR, and value.

hbond_constraint() [1/2]

virtual void HbondZinc::hbond_constraint ( core::pose::Pose &  pose, Size  hbond_res, Size  aa_index, Size  primary_shell_index, Size  krot  )

inlinevirtual

References numeric::angle_of(), backrub_iterations, basic::options::OptionKeys::constraints::constraints, numeric::conversions::degrees(), dist(), numeric::xyzVector< T >::distance(), vancomycin::min_mover, beta_nonlocal::mm, localrmsd::output_name, basic::options::OptionKeys::backrub::pivot_atoms, basic::options::OptionKeys::backrub::pivot_residues, beta_nonlocal::pose, numeric::conversions::radians(), oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, and TR.

hbond_constraint() [2/2]

virtual void HbondZinc::hbond_constraint ( core::pose::Pose &  pose, Size  hbond_res, Size  aa_index, Size  primary_shell_index, Size  krot  )

inlinevirtual

References numeric::angle_of(), basic::options::OptionKeys::constraints::constraints, numeric::conversions::degrees(), dist(), numeric::xyzVector< T >::distance(), vancomycin::min_mover, beta_nonlocal::mm, localrmsd::output_name, beta_nonlocal::pose, numeric::conversions::radians(), oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, and TR.

repack() [1/4]

virtual void HbondZinc::repack ( core::pose::Pose &  pose )

inlinevirtual

References pyrosetta::create_score_function, create_a3b_hbs::i, basic::options::option, beta_nonlocal::pose, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, vancomycin::task, TR, and basic::options::OptionKeys::packing::use_input_sc.

repack() [2/4]

virtual void HbondZinc::repack ( core::pose::Pose &  pose )

inlinevirtual

References pyrosetta::create_score_function, create_a3b_hbs::i, beta_nonlocal::pose, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, vancomycin::task, and TR.

repack() [3/4]

virtual void HbondZinc::repack ( core::pose::Pose &  pose )

inlinevirtual

References pyrosetta::create_score_function, create_a3b_hbs::i, beta_nonlocal::pose, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, vancomycin::task, and TR.

repack() [4/4]

virtual void HbondZinc::repack ( core::pose::Pose &  pose )

inlinevirtual

References pyrosetta::create_score_function, create_a3b_hbs::i, basic::options::option, beta_nonlocal::pose, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, vancomycin::task, TR, and basic::options::OptionKeys::packing::use_input_sc.

Member Data Documentation

backsideO_His_

Size HbondZinc::backsideO_His_

private

match_pose_

core::pose::Pose HbondZinc::match_pose_

private

msr_

utility::vector1< protocols::metal_interface::MetalSiteResidueOP > HbondZinc::msr_

private

primary_shell_neighbors_

utility::vector1< utility::vector1< Size > > HbondZinc::primary_shell_neighbors_

private

starting_pose_

core::pose::Pose HbondZinc::starting_pose_

private

---

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

• src/apps/pilot/bder/HbondZinc.cc
• src/apps/pilot/bder/HbondZinc_allpolar.cc
• src/apps/pilot/bder/HbondZinc_ser.cc
• src/apps/pilot/bder/HbondZincHHHO.cc