xtal_water_bunsat Class Reference

Inheritance diagram for xtal_water_bunsat:

Public Member Functions
	xtal_water_bunsat ()
virtual	~xtal_water_bunsat ()
virtual void	apply (core::pose::Pose &pose)
virtual bool	atomid_is_contacting_crystallographic_water (id::AtomID atid)
virtual Real	check_sasa (id::AtomID atid)
virtual std::string	get_name () const
	xtal_water_bunsat ()
virtual	~xtal_water_bunsat ()
virtual void	apply (core::pose::Pose &pose)
virtual core::Real	closest_crystallographic_water_dist (core::pose::Pose const &dry_pose, id::AtomID const atid, utility::vector1< point > const &water_points)
virtual Real	check_sasa (core::pose::Pose const &, id::AtomID const atid, basic::MetricValue< core::id::AtomID_Map< core::Real > > const &atom_sasa)
virtual std::string	get_name () const
	xtal_water_bunsat ()
	~xtal_water_bunsat ()
std::string	get_name () const
void	apply (core::pose::Pose &pose,)
	xtal_water_bunsat ()
virtual	~xtal_water_bunsat ()
virtual std::string	get_name () const
virtual void	apply (core::pose::Pose &pose)

Private Member Functions
virtual void	report_sasa_if_contacting_water (core::pose::Pose const &dry_pose, core::Size const resi, std::string const &atom_name, basic::MetricValue< core::id::AtomID_Map< core::Real > > const &atom_sasa, utility::vector1< point > const &water_points, core::Real const max_dist_contact)
bool	evaluate_hbond_geom (Real AHdist, Real AHD)

Private Attributes
basic::MetricValue< core::id::AtomID_Map< core::Real > >	atom_sasa_
utility::vector1< point >	water_points_
core::pose::Pose	dry_pose_

Static Private Attributes
static constexpr const Real	AHdist_geom_eval_threshold = 2.8
static constexpr const Real	AHD_geom_eval_threshold = 90

Constructor & Destructor Documentation

xtal_water_bunsat() [1/4]

xtal_water_bunsat::xtal_water_bunsat ( )

inline

~xtal_water_bunsat() [1/4]

virtual xtal_water_bunsat::~xtal_water_bunsat ( )

inlinevirtual

xtal_water_bunsat() [2/4]

xtal_water_bunsat::xtal_water_bunsat ( )

inline

~xtal_water_bunsat() [2/4]

virtual xtal_water_bunsat::~xtal_water_bunsat ( )

inlinevirtual

xtal_water_bunsat() [3/4]

xtal_water_bunsat::xtal_water_bunsat ( )

inline

~xtal_water_bunsat() [3/4]

xtal_water_bunsat::~xtal_water_bunsat ( )

inline

xtal_water_bunsat() [4/4]

xtal_water_bunsat::xtal_water_bunsat ( )

inline

~xtal_water_bunsat() [4/4]

virtual xtal_water_bunsat::~xtal_water_bunsat ( )

inlinevirtual

Member Function Documentation

apply() [1/4]

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

inlinevirtual

References create_a3b_hbs::i, basic::options::option, beta_nonlocal::pose, oop_conformations::scorefxn, TR, and use_varsoldist_sasa_calc.

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

apply() [2/4]

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

inlinevirtual

References end, utility::vector1< T, A >::has_value(), create_a3b_hbs::i, num_chains(), basic::options::option, beta_nonlocal::pose, oop_conformations::scorefxn, erraser_analysis::temp, TR, use_varsoldist_sasa_calc, water_dist_H, and water_dist_O.

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

apply() [3/4]

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

inlinevirtual

References utility::io::oc::cout, dist(), end, lactamize::filename, utility::io::ocstream::flush(), create_a3b_hbs::i, max(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, create_a3b_hbs::pdb_info, beta_nonlocal::pose, bur_nodon_tyr::probe_radius, res, oop_conformations::scorefxn, and w.

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

apply() [4/4]

void xtal_water_bunsat::apply ( core::pose::Pose &  pose )

inline

References utility::io::oc::cout, find_neighbors(), h, test.T200_Scoring::hbond_set, basic::options::OptionKeys::legacy_sewing::neighbor_cutoff, create_a3b_hbs::nres, create_a3b_hbs::pdb_info, beta_nonlocal::pose, res, and oop_conformations::scorefxn.

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

atomid_is_contacting_crystallographic_water()

virtual bool xtal_water_bunsat::atomid_is_contacting_crystallographic_water ( id::AtomID  atid )

inlinevirtual

References numeric::xyzVector< T >::distance(), basic::options::OptionKeys::contactMap::distance_cutoff, create_a3b_hbs::i, and TR.

check_sasa() [1/2]

virtual Real xtal_water_bunsat::check_sasa ( core::pose::Pose const &  , id::AtomID const  atid, basic::MetricValue< core::id::AtomID_Map< core::Real > > const &  atom_sasa  )

inlinevirtual

check_sasa() [2/2]

virtual Real xtal_water_bunsat::check_sasa ( id::AtomID  atid )

inlinevirtual

closest_crystallographic_water_dist()

virtual core::Real xtal_water_bunsat::closest_crystallographic_water_dist ( core::pose::Pose const &  dry_pose, id::AtomID const  atid, utility::vector1< point > const &  water_points  )

inlinevirtual

References numeric::xyzVector< T >::distance(), and create_a3b_hbs::i.

evaluate_hbond_geom()

bool xtal_water_bunsat::evaluate_hbond_geom ( Real  AHdist, Real  AHD  )

inlineprivate

get_name() [1/4]

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

inlinevirtual

get_name() [2/4]

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

inlinevirtual

get_name() [3/4]

std::string xtal_water_bunsat::get_name ( ) const

inline

get_name() [4/4]

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

inlinevirtual

report_sasa_if_contacting_water()

virtual void xtal_water_bunsat::report_sasa_if_contacting_water ( core::pose::Pose const &  dry_pose, core::Size const  resi, std::string const &  atom_name, basic::MetricValue< core::id::AtomID_Map< core::Real > > const &  atom_sasa, utility::vector1< point > const &  water_points, core::Real const  max_dist_contact  )

inlineprivatevirtual

References basic::options::OptionKeys::optE::fixed, pna::resi, and TR.

Member Data Documentation

AHD_geom_eval_threshold

constexpr const Real xtal_water_bunsat::AHD_geom_eval_threshold = 90

staticconstexprprivate

AHdist_geom_eval_threshold

constexpr const Real xtal_water_bunsat::AHdist_geom_eval_threshold = 2.8

staticconstexprprivate

atom_sasa_

basic::MetricValue< core::id::AtomID_Map< core::Real > > xtal_water_bunsat::atom_sasa_

private

dry_pose_

core::pose::Pose xtal_water_bunsat::dry_pose_

private

water_points_

utility::vector1<point> xtal_water_bunsat::water_points_

private

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

• src/apps/pilot/bder/xtal_water_bunsat.cc
• src/apps/pilot/kevin/read_l_print_pdbinfo.cc
• src/apps/pilot/kevin/khXtal_water_bunsat.cc
• src/apps/pilot/kevin/wat_distances.cc