#include <ImplicitFastClashCheck.hh>

Public Member Functions
virtual	~ImplicitFastClashCheck ()
	Automatically generated virtual destructor for class deriving directly from ReferenceCount. More...

	ImplicitFastClashCheck (core::pose::Pose const &pose_in, core::Real clash_dis)

	ImplicitFastClashCheck (core::pose::Pose const &pose_in, core::Real clash_dis, utility::vector1< core::Size > ignore)

	ImplicitFastClashCheck (utility::vector1< core::pose::Pose > const &poses_in, core::Real clash_dis, utility::vector1< core::Size > ignore)

void	init_clash_check (utility::vector1< core::pose::Pose > const &poses, core::Real neighbor_cutoff, utility::vector1< core::Size > ignore)

bool	clash_check (numeric::xyzVector< core::Real > const &pp) const

platform::uint	clash_count (numeric::xyzVector< core::Real > const &pp) const

bool	clash_check (numeric::xyzVector< core::Real > const &pp, core::Size resno) const

bool	clash_check_trimer (core::pose::Pose const &pose, Size refrsd) const

void	dump_debug_pdb (utility::io::ozstream &out, core::kinematics::Stub const &stub, char chain= 'Z') const

void	dump_debug_pdb (std::string const &fname, core::kinematics::Stub const &stub, char chain= 'Z') const

bool	clash_check_test (numeric::xyzVector< core::Real > const &pp) const

core::Size	size ()

Private Attributes
core::pose::PoseCOP	pose_

utility::vector1 < numeric::xyzVector < core::Real > >	points_

utility::vector1< core::Size >	resno_

utility::vector1< core::Size >	atomno_

ObjexxFCL::FArray3D < utility::vector1< unsigned int > >	cubes_

numeric::xyzVector< core::Real >	bbl_

numeric::xyzTriple< core::Size >	cube_dim_

core::Real	side_inv_

core::Real	neighbor_cutoff_

core::Real	neighbor_cutoff_sq_

ObjexxFCL::FArray3D < utility::vector1 < numeric::xyzVector < core::Real > > >	cubes_ca_

numeric::xyzVector< core::Real >	bbl_ca_

numeric::xyzTriple< core::Size >	cube_dim_ca_

core::Real	side_inv_ca_

core::Real	neighbor_cutoff_ca_

core::Real	neighbor_cutoff_sq_ca_

Constructor & Destructor Documentation

protocols::scoring::ImplicitFastClashCheck::~ImplicitFastClashCheck ( )

virtual

Automatically generated virtual destructor for class deriving directly from ReferenceCount.

Auto-generated virtual destructor

protocols::scoring::ImplicitFastClashCheck::ImplicitFastClashCheck	(	core::pose::Pose const &	pose_in,
		core::Real	clash_dis
	)

protocols::scoring::ImplicitFastClashCheck::ImplicitFastClashCheck	(	core::pose::Pose const &	pose_in,
		core::Real	clash_dis,
		utility::vector1< core::Size >	ignore
	)

protocols::scoring::ImplicitFastClashCheck::ImplicitFastClashCheck	(	utility::vector1< core::pose::Pose > const &	poses_in,
		core::Real	clash_dis,
		utility::vector1< core::Size >	ignore
	)

Member Function Documentation

bool protocols::scoring::ImplicitFastClashCheck::clash_check ( numeric::xyzVector< core::Real > const & pp ) const

Referenced by protocols::kinmatch::BruteFunGroupTK::place_c(), protocols::kinmatch::BruteFunGroupTK::place_d(), and protocols::kinmatch::BruteFunGroupTK::place_h().

bool protocols::scoring::ImplicitFastClashCheck::clash_check	(	numeric::xyzVector< core::Real > const &	pp,
		core::Size	resno
	)		const

bool protocols::scoring::ImplicitFastClashCheck::clash_check_test ( numeric::xyzVector< core::Real > const & pp ) const

References numeric::xyzVector< class >::distance_squared(), and utility_exit_with_message.

bool protocols::scoring::ImplicitFastClashCheck::clash_check_trimer	(	core::pose::Pose const &	pose,
		Size	refrsd
	)		const

References core::conformation::Residue::nheavyatoms(), core::pose::Pose::residue(), rot(), numeric::rotation_matrix_degrees(), core::pose::Pose::xyz(), and protocols::kinmatch::xyz().

platform::uint protocols::scoring::ImplicitFastClashCheck::clash_count ( numeric::xyzVector< core::Real > const & pp ) const

References begin, numeric::xyzVector< class >::distance_squared(), end, max(), min, size(), numeric::xyzVector< class >::x(), numeric::xyzVector< class >::y(), and numeric::xyzVector< class >::z().

void protocols::scoring::ImplicitFastClashCheck::dump_debug_pdb	(	utility::io::ozstream &	out,
		core::kinematics::Stub const &	stub,
		char	chain = `'Z'`
	)		const

References F, core::kinematics::Stub::global2local(), I, numeric::xyzVector< class >::x(), numeric::xyzVector< class >::y(), and numeric::xyzVector< class >::z().

void protocols::scoring::ImplicitFastClashCheck::dump_debug_pdb	(	std::string const &	fname,
		core::kinematics::Stub const &	stub,
		char	chain = `'Z'`
	)		const

References out.

void protocols::scoring::ImplicitFastClashCheck::init_clash_check	(	utility::vector1< core::pose::Pose > const &	poses,
		core::Real	neighbor_cutoff,
		utility::vector1< core::Size >	ignore
	)

References numeric::max(), numeric::xyzVector< class >::max(), numeric::min(), numeric::xyzVector< class >::min(), pi, numeric::square(), numeric::xyzVector< class >::x(), numeric::xyzVector< class >::y(), and numeric::xyzVector< class >::z().

core::Size protocols::scoring::ImplicitFastClashCheck::size ( )

inline

References points_.

Member Data Documentation

utility::vector1<core::Size> protocols::scoring::ImplicitFastClashCheck::atomno_

private

numeric::xyzVector<core::Real> protocols::scoring::ImplicitFastClashCheck::bbl_

private

numeric::xyzVector<core::Real> protocols::scoring::ImplicitFastClashCheck::bbl_ca_

private

numeric::xyzTriple< core::Size > protocols::scoring::ImplicitFastClashCheck::cube_dim_

private

numeric::xyzTriple< core::Size > protocols::scoring::ImplicitFastClashCheck::cube_dim_ca_

private

ObjexxFCL::FArray3D< utility::vector1<unsigned int> > protocols::scoring::ImplicitFastClashCheck::cubes_

private

ObjexxFCL::FArray3D< utility::vector1<numeric::xyzVector<core::Real> > > protocols::scoring::ImplicitFastClashCheck::cubes_ca_

private

core::Real protocols::scoring::ImplicitFastClashCheck::neighbor_cutoff_

private

core::Real protocols::scoring::ImplicitFastClashCheck::neighbor_cutoff_ca_

private

core::Real protocols::scoring::ImplicitFastClashCheck::neighbor_cutoff_sq_

private

core::Real protocols::scoring::ImplicitFastClashCheck::neighbor_cutoff_sq_ca_

private

utility::vector1<numeric::xyzVector<core::Real> > protocols::scoring::ImplicitFastClashCheck::points_

private

Referenced by size().

core::pose::PoseCOP protocols::scoring::ImplicitFastClashCheck::pose_

private

utility::vector1<core::Size> protocols::scoring::ImplicitFastClashCheck::resno_

private

core::Real protocols::scoring::ImplicitFastClashCheck::side_inv_

private

core::Real protocols::scoring::ImplicitFastClashCheck::side_inv_ca_

private

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

src/protocols/scoring/ImplicitFastClashCheck.hh
src/protocols/scoring/ImplicitFastClashCheck.cc

Public Member Functions

Private Attributes

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation