apps::pilot::momeara::HBondConformation Class Reference

Public Member Functions
	HBondConformation ()
	~HBondConformation ()
	HBondConformation (HBondConformation const &src)
HBondConformation const &	operator= (HBondConformation const &src)
PoseOP	make_conformation (HBSeqSep const seq_sep, Residue &don_rsd, Size const hatm, Residue &acc_rsd, Size const &aatm, RT const &hbond_geometry) const
Stub	build_donor_frame (Residue const &rsd, Size const &hatm) const
Stub	build_acceptor_frame (Residue const &rsd, Size const &aatm) const
void	relax_pose_around_hbond (PoseOP pose, ScoreFunctionOP scfxn, Size const don_seqpos, Size const hatm, Size const acc_seqpos, Size const aatm, Real const well_depth=0, Real slope=400) const
void	example_OH_pose () const
vector1< PoseOP >	hbond_param_sweep (HBSeqSep const seq_sep, ResidueOP const &don_rsd, Size const hatm, ResidueOP const &acc_rsd, Size const &aatm, string const &pose_name_prefix, Size steps) const
ResidueOP	build_residue (ResidueTypeSetCAP residue_type_set, std::string const &res_name3, bool const uterm_cap=true, bool const lterm_cap=true)
vector1< PoseOP >	run_example_hbond_sweep (string const &don_res_name, string const &hatm_name, string const &acc_res_name, string const &aatm_name, Size steps)
void	score_conformations (vector1< PoseOP > features)

Constructor & Destructor Documentation

HBondConformation() [1/2]

apps::pilot::momeara::HBondConformation::HBondConformation ( )

inline

~HBondConformation()

apps::pilot::momeara::HBondConformation::~HBondConformation ( )

inline

HBondConformation() [2/2]

apps::pilot::momeara::HBondConformation::HBondConformation

(

HBondConformation const &

src

)

Member Function Documentation

build_acceptor_frame()

Stub apps::pilot::momeara::HBondConformation::build_acceptor_frame ( Residue const &  rsd, Size const &  aatm  ) const

inline

References enumerate_junctions::default, and apps::pilot::momeara::tr.

build_donor_frame()

Stub apps::pilot::momeara::HBondConformation::build_donor_frame ( Residue const &  rsd, Size const &  hatm  ) const

inline

build_residue()

ResidueOP apps::pilot::momeara::HBondConformation::build_residue ( ResidueTypeSetCAP  residue_type_set, std::string const &  res_name3, bool const  uterm_cap = true, bool const  lterm_cap = true  )

inline

References pyrosetta.utility.array::message, basic::options::OptionKeys::in::file::residue_type_set, apps::pilot::momeara::tr, and utility_exit_with_message.

example_OH_pose()

void apps::pilot::momeara::HBondConformation::example_OH_pose ( ) const

inline

References basic::Tracer::Debug, create_a3b_hbs::i, create_a3b_hbs::j, create_a3b_hbs::k, beta_nonlocal::pose, basic::options::OptionKeys::in::file::residue_type_set, and apps::pilot::momeara::tr.

Referenced by main().

hbond_param_sweep()

vector1< PoseOP > apps::pilot::momeara::HBondConformation::hbond_param_sweep ( HBSeqSep const  seq_sep, ResidueOP const &  don_rsd, Size const  hatm, ResidueOP const &  acc_rsd, Size const &  aatm, string const &  pose_name_prefix, Size  steps  ) const

inline

References basic::Tracer::Debug, pyrosetta.distributed.io::get_score_function(), basic::options::OptionKeys::mp::mutate_relax::nmodels, create_a3b_hbs::pdb_info, beta_nonlocal::pose, correlation_time::steps, apps::pilot::momeara::tr, numeric::xyzVector< T >::x(), numeric::xyzVector< T >::y(), and numeric::xyzVector< T >::z().

make_conformation()

PoseOP apps::pilot::momeara::HBondConformation::make_conformation ( HBSeqSep const  seq_sep, Residue &  don_rsd, Size const  hatm, Residue &  acc_rsd, Size const &  aatm, RT const &  hbond_geometry  ) const

inline

References a, compute_difference::b, kmeans_adaptive_kernel_density_bb_dependent_rotlib::c, basic::Tracer::Debug, enumerate_junctions::default, beta_nonlocal::pose, basic::options::OptionKeys::in::file::residue_type_set, challenge::ss, and apps::pilot::momeara::tr.

operator=()

HBondConformation const& apps::pilot::momeara::HBondConformation::operator=

(

HBondConformation const &

src

)

relax_pose_around_hbond()

void apps::pilot::momeara::HBondConformation::relax_pose_around_hbond ( PoseOP  pose, ScoreFunctionOP  scfxn, Size const  don_seqpos, Size const  hatm, Size const  acc_seqpos, Size const  aatm, Real const  well_depth = 0, Real  slope = 400  ) const

inline

References spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::A, ObjexxFCL::abs(), spectral_cluster_kmeans_adaptive_kernel_density_bb_dependent_rotlib::D, basic::Tracer::Debug, build_jacobian::distance, numeric::xyzVector< T >::distance(), func, hist2d::H, pyrosetta.utility.array::message, vancomycin::min_mover, basic::options::OptionKeys::dna::specificity::min_type, basic::options::OptionKeys::in::file::movemap, basic::options::option, beta_nonlocal::pose, revert_app::threshold, basic::options::OptionKeys::loops::ccd::tolerance, apps::pilot::momeara::tr, and utility_exit_with_message.

run_example_hbond_sweep()

vector1<PoseOP> apps::pilot::momeara::HBondConformation::run_example_hbond_sweep ( string const &  don_res_name, string const &  hatm_name, string const &  acc_res_name, string const &  aatm_name, Size  steps  )

inline

References basic::options::option, basic::options::OptionKeys::out::prefix, basic::options::OptionKeys::in::file::residue_type_set, correlation_time::steps, apps::pilot::momeara::tr, and basic::options::OptionKeys::inout::dbms::user.

Referenced by main().

score_conformations()

void apps::pilot::momeara::HBondConformation::score_conformations ( vector1< PoseOP >  features )

inline

References pyrosetta.distributed.io::get_score_function(), legacy_score_vs_rmsd::scores, and apps::pilot::momeara::tr.

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

• src/apps/pilot/momeara/hbond_param_sweep.cc