cryst_reporters.hh File Reference

#include <protocols/cryst/refinable_lattice.hh>
#include <utility/graph/Graph.hh>
#include <core/scoring/sc/ShapeComplementarityCalculator.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/EnergyGraph.hh>
#include <core/scoring/hbonds/HBondSet.hh>
#include <core/scoring/hbonds/hbonds.hh>
#include <core/scoring/hbonds/HBondOptions.hh>
#include <core/scoring/sasa.hh>
#include <core/scoring/methods/EnergyMethodOptions.hh>
#include <core/chemical/AtomType.hh>
#include <core/pose/init_id_map.hh>
#include <core/pose/symmetry/util.hh>
#include <core/conformation/symmetry/SymmetryInfo.hh>
#include <core/conformation/symmetry/SymmetricConformation.hh>
#include <protocols/relax/FastRelax.hh>
#include <utility/tools/make_map.hh>
#include <numeric/xyzMatrix.hh>
#include <numeric/xyzVector.hh>
#include <numeric/random/random.hh>
#include <basic/options/keys/OptionKeys.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/kinematics/MoveMap.hh>
#include <basic/Tracer.hh>

Classes
struct	SingleInterface

Typedefs
typedef utility::vector1< core::Size >	Sizes
typedef numeric::xyzMatrix< core::Real >	Matrix

Functions
template<class T >
bool	has_element (utility::vector1< T > const &list, T elt)
template<class T >
bool	has_element (T elt, utility::vector1< T > const &list)
Vector	random_unit_vector ()
void	randomly_shift_and_tilt_pose (Pose &pose)
void	randomly_shift_and_tilt_poses (Pose &pose1, Pose &pose2)
bool	transforms_equiv (numeric::xyzMatrix< Real > const &S1, numeric::xyzVector< Real > const &T1, numeric::xyzMatrix< Real > const &S2, numeric::xyzVector< Real > const &T2)
core::Real	get_max_interface (Pose, utility::vector1< SingleInterface > &allInterfaces, utility::vector1< core::kinematics::RT > const &)
void	reconstruct_lattice_pose_info (core::Size const nres_monomer, core::pose::Pose const &pose, core::Size &base_monomer, core::Size &num_monomers, utility::vector1< core::Size > &monomer_jumps, utility::vector1< core::Size > &monomer_anchor_virtuals)
core::Real	get_interface_score (Pose, utility::vector1< SingleInterface > &allInterfaces, utility::vector1< core::kinematics::RT > const &rts_all, bool verbose=false)
Real	calc_solvent_content (Real const vm)
Real	calc_vm (Real const volume, std::string const &sequence, Size const ncopies)
void	get_sc (protocols::cryst::MakeLatticeMover &setup, core::pose::Pose &pose, core::Real &total_sc, core::Real &weakest_sc, core::Real &total_sasa, core::Real &weakest_sasa)
void	single_sasa_calc (core::pose::Pose &pose, core::Real probe_radius, core::Real &total_sasa, core::Real &total_nonpolar_sasa)
void	get_sasa (protocols::cryst::MakeLatticeMover &setup, core::pose::Pose &pose, core::Real &total_sasa, core::Real &weakest_sasa, core::Real &total_nonpolar_sasa, core::Real &weakest_nonpolar_sasa)
void	find_buried_unsatisfied_polars (Pose const &pose_in, core::Size nres_asu, utility::vector1< id::AtomID > &buried_unsatisfied_donors, utility::vector1< id::AtomID > &buried_unsatisfied_acceptors, Real const probe_radius=1.0)
	skips non-protein More...
core::Real	unsatisfied_buried_polars (core::pose::Pose &pose, core::scoring::ScoreFunctionOP sf, core::Real probe, utility::vector1< bool > &scs_buried)
core::Real	unsatisfied_buried_polars (core::pose::Pose &pose, core::scoring::ScoreFunctionOP sf, core::Real probe)
void	get_perresE (core::pose::Pose &pose, core::scoring::ScoreFunctionOP sf, utility::vector1< core::Real > &perresE, bool int_only)
void	do_sc_relax (core::pose::Pose &pose, core::scoring::ScoreFunctionOP sf, utility::vector1< bool > residues, bool rb, int rpts=1)
void	do_sc_relax (core::pose::Pose &pose, core::scoring::ScoreFunctionOP sf, bool rb, int rpts=1)
void	do_sc_min (core::pose::Pose &pose, core::scoring::ScoreFunctionOP sf, utility::vector1< bool > residues, bool rb, int rpts=1)
core::Real	ddg (core::pose::Pose &pose, core::scoring::ScoreFunctionOP sf, utility::vector1< core::Real > &perresddg, core::Real &esymm, core::Real &easymm, int ncyc=1, int nrepeats=3)
void	get_interface_energies (protocols::cryst::MakeLatticeMover &setup, core::pose::Pose &pose, core::scoring::ScoreFunctionOP sf, core::Real &totalE, core::Real &intE, core::Real &weakestE)

Variables
static basic::Tracer	TS ("cryst.reporters")

Typedef Documentation

Matrix

typedef numeric::xyzMatrix< core::Real > Matrix

Sizes

typedef utility::vector1< core::Size > Sizes

Function Documentation

calc_solvent_content()

Real calc_solvent_content

(

Real const

vm

)

calc_vm()

Real calc_vm	(	Real const	volume,
		std::string const &	sequence,
		Size const	ncopies
	)

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::c, utility::tools::make_map(), basic::options::OptionKeys::relax::sequence, and basic::options::OptionKeys::sc::weight.

ddg()

core::Real ddg	(	core::pose::Pose &	pose,
		core::scoring::ScoreFunctionOP	sf,
		utility::vector1< core::Real > &	perresddg,
		core::Real &	esymm,
		core::Real &	easymm,
		int	ncyc = 1,
		int	nrepeats = 3
	)

References utility::options::FileOptionKey::clone(), do_sc_relax(), get_perresE(), create_a3b_hbs::i, enumerate_junctions::int, beta_nonlocal::pose, and basic::options::OptionKeys::out::sf.

do_sc_min()

void do_sc_min	(	core::pose::Pose &	pose,
		core::scoring::ScoreFunctionOP	sf,
		utility::vector1< bool >	residues,
		bool	rb,
		int	rpts = 1
	)

References create_a3b_hbs::i, basic::options::OptionKeys::in::file::movemap, beta_nonlocal::pose, execute::residues, and basic::options::OptionKeys::out::sf.

do_sc_relax() [1/2]

void do_sc_relax	(	core::pose::Pose &	pose,
		core::scoring::ScoreFunctionOP	sf,
		bool	rb,
		int	rpts = 1
	)

References basic::options::OptionKeys::in::file::movemap, beta_nonlocal::pose, and basic::options::OptionKeys::out::sf.

do_sc_relax() [2/2]

void do_sc_relax	(	core::pose::Pose &	pose,
		core::scoring::ScoreFunctionOP	sf,
		utility::vector1< bool >	residues,
		bool	rb,
		int	rpts = 1
	)

References create_a3b_hbs::i, basic::options::OptionKeys::in::file::movemap, beta_nonlocal::pose, execute::residues, and basic::options::OptionKeys::out::sf.

Referenced by ddg().

find_buried_unsatisfied_polars()

void find_buried_unsatisfied_polars	(	Pose const &	pose_in,
		core::Size	nres_asu,
		utility::vector1< id::AtomID > &	buried_unsatisfied_donors,
		utility::vector1< id::AtomID > &	buried_unsatisfied_acceptors,
		Real const	probe_radius = 1.0
	)

skips non-protein

References test.T200_Scoring::hbond_set, create_a3b_hbs::i, beta_nonlocal::pose, bur_nodon_tyr::probe_radius, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::out::sf, and basic::options::OptionKeys::symmetry::symmetry.

Referenced by unsatisfied_buried_polars().

get_interface_energies()

void get_interface_energies	(	protocols::cryst::MakeLatticeMover &	setup,
		core::pose::Pose &	pose,
		core::scoring::ScoreFunctionOP	sf,
		core::Real &	totalE,
		core::Real &	intE,
		core::Real &	weakestE
	)

References utility::options::FileOptionKey::clone(), get_interface_score(), utility::graph::Edge::get_node(), create_a3b_hbs::i, enumerate_junctions::int, create_a3b_hbs::j, beta_nonlocal::pose, test.T200_Scoring::rsd1, test.T200_Scoring::rsd2, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::out::sf, basic::options::OptionKeys::symmetry::symmetry, and utility::graph::Node::upper_edge_list_end().

Referenced by CrystRelax::apply(), CrystDesign::do_reversion(), CrystDesign::filter_and_report(), and CrystDesign::greedy_revert_unsats().

get_interface_score()

core::Real get_interface_score	(	Pose	,
		utility::vector1< SingleInterface > &	allInterfaces,
		utility::vector1< core::kinematics::RT > const &	rts_all,
		bool	verbose = false
	)

References utility::io::oc::cerr, gpu_set_args::done, create_a3b_hbs::i, enumerate_junctions::int, create_a3b_hbs::j, create_a3b_hbs::k, min(), numeric::xyzMatrix< T >::rows(), create_a3b_hbs::score, transforms_equiv(), basic::options::OptionKeys::sc::verbose, numeric::xyzMatrix< T >::xx(), numeric::xyzMatrix< T >::xy(), numeric::xyzMatrix< T >::xz(), numeric::xyzMatrix< T >::yx(), numeric::xyzMatrix< T >::yy(), numeric::xyzMatrix< T >::yz(), numeric::xyzMatrix< T >::zx(), numeric::xyzMatrix< T >::zy(), and numeric::xyzMatrix< T >::zz().

Referenced by CrystFFTDock::apply(), get_interface_energies(), get_sasa(), and get_sc().

get_max_interface()

core::Real get_max_interface	(	Pose	,
		utility::vector1< SingleInterface > &	allInterfaces,
		utility::vector1< core::kinematics::RT > const &
	)

References enumerate_junctions::int, create_a3b_hbs::k, and max().

get_perresE()

void get_perresE	(	core::pose::Pose &	pose,
		core::scoring::ScoreFunctionOP	sf,
		utility::vector1< core::Real > &	perresE,
		bool	int_only
	)

References utility::options::FileOptionKey::clone(), utility::graph::Edge::get_node(), create_a3b_hbs::i, create_a3b_hbs::j, beta_nonlocal::pose, test.T200_Scoring::rsd1, test.T200_Scoring::rsd2, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::out::sf, basic::options::OptionKeys::symmetry::symmetry, and utility::graph::Node::upper_edge_list_end().

Referenced by ddg().

get_sasa()

void get_sasa	(	protocols::cryst::MakeLatticeMover &	setup,
		core::pose::Pose &	pose,
		core::Real &	total_sasa,
		core::Real &	weakest_sasa,
		core::Real &	total_nonpolar_sasa,
		core::Real &	weakest_nonpolar_sasa
	)

References basic::options::OptionKeys::AnchoredDesign::anchor, get_interface_score(), create_a3b_hbs::i, beta_nonlocal::pose, basic::options::OptionKeys::frags::scoring::scoring, single_sasa_calc(), basic::options::OptionKeys::cutoutdomain::start, and basic::options::OptionKeys::symmetry::symmetry.

Referenced by CrystDesign::do_reversion(), CrystDesign::filter_and_report(), harvest_motifs(), and sicdock_thread_num().

get_sc()

void get_sc	(	protocols::cryst::MakeLatticeMover &	setup,
		core::pose::Pose &	pose,
		core::Real &	total_sc,
		core::Real &	weakest_sc,
		core::Real &	total_sasa,
		core::Real &	weakest_sasa
	)

References test.T009_Exceptions::e, get_interface_score(), create_a3b_hbs::i, create_a3b_hbs::j, beta_nonlocal::pose, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::cutoutdomain::start, and basic::options::OptionKeys::symmetry::symmetry.

Referenced by CrystDesign::do_reversion(), and CrystDesign::filter_and_report().

has_element() [1/2]

template<class T >

bool has_element	(	T	elt,
		utility::vector1< T > const &	list
	)

References has_element(), and basic::options::OptionKeys::in::file::list.

has_element() [2/2]

template<class T >

bool has_element	(	utility::vector1< T > const &	list,
		T	elt
	)

References detail::find(), and basic::options::OptionKeys::in::file::list.

Referenced by has_element(), and unsatisfied_buried_polars().

random_unit_vector()

Vector random_unit_vector

(

)

References oop_conformations::phi, numeric::constants::d::pi, numeric::sin_cos_range(), and numeric::random::uniform().

Referenced by randomly_shift_and_tilt_pose(), and randomly_shift_and_tilt_poses().

randomly_shift_and_tilt_pose()

void randomly_shift_and_tilt_pose

(

Pose &

pose

)

References cols(), beta_nonlocal::pose, docking::R, random_unit_vector(), runtime_assert, numeric::random::uniform(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::v, x, predPRE::y, and predPRE::z.

randomly_shift_and_tilt_poses()

void randomly_shift_and_tilt_poses	(	Pose &	pose1,
		Pose &	pose2
	)

References cols(), test.T008_Serialization::pose1, test.T008_Serialization::pose2, docking::R, random_unit_vector(), runtime_assert, numeric::random::uniform(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::v, x, predPRE::y, and predPRE::z.

Referenced by unsatisfied_buried_polars().

reconstruct_lattice_pose_info()

void reconstruct_lattice_pose_info	(	core::Size const	nres_monomer,
		core::pose::Pose const &	pose,
		core::Size &	base_monomer,
		core::Size &	num_monomers,
		utility::vector1< core::Size > &	monomer_jumps,
		utility::vector1< core::Size > &	monomer_anchor_virtuals
	)

References test.T009_Exceptions::e, create_a3b_hbs::f, basic::Tracer::Fatal, create_a3b_hbs::j, offset, beta_nonlocal::pose, runtime_assert, TS, and utility_exit_with_message.

single_sasa_calc()

void single_sasa_calc	(	core::pose::Pose &	pose,
		core::Real	probe_radius,
		core::Real &	total_sasa,
		core::Real &	total_nonpolar_sasa
	)

References create_a3b_hbs::i, create_a3b_hbs::j, beta_nonlocal::pose, and bur_nodon_tyr::probe_radius.

Referenced by get_sasa().

transforms_equiv()

bool transforms_equiv ( numeric::xyzMatrix< Real > const &  S1, numeric::xyzVector< Real > const &  T1, numeric::xyzMatrix< Real > const &  S2, numeric::xyzVector< Real > const &  T2  )

inline

References test.T009_Exceptions::e, create_a3b_hbs::i, create_a3b_hbs::j, and revert_app::threshold.

Referenced by get_interface_score().

unsatisfied_buried_polars() [1/2]

core::Real unsatisfied_buried_polars	(	core::pose::Pose &	pose,
		core::scoring::ScoreFunctionOP	sf,
		core::Real	probe
	)

References beta_nonlocal::pose, basic::options::OptionKeys::out::sf, and unsatisfied_buried_polars().

unsatisfied_buried_polars() [2/2]

core::Real unsatisfied_buried_polars	(	core::pose::Pose &	pose,
		core::scoring::ScoreFunctionOP	sf,
		core::Real	probe,
		utility::vector1< bool > &	scs_buried
	)

References utility::options::FileOptionKey::clone(), find_buried_unsatisfied_polars(), has_element(), create_a3b_hbs::i, create_a3b_hbs::increment, create_a3b_hbs::j, my_options::nrepeat, beta_nonlocal::pose, docking::R, randomly_shift_and_tilt_poses(), basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::out::sf, and basic::options::OptionKeys::symmetry::symmetry.

Referenced by CrystDesign::do_reversion(), CrystDesign::filter_and_report(), CrystDesign::greedy_revert_unsats(), and unsatisfied_buried_polars().

Variable Documentation

TS

basic::Tracer TS("cryst.reporters") ( "cryst.reporters"  )

static

Referenced by reconstruct_lattice_pose_info().