protocols::scoring::ImplicitFastClashCheck Class Reference

#include <ImplicitFastClashCheck.hh>

Inheritance diagram for protocols::scoring::ImplicitFastClashCheck:

Collaboration diagram for protocols::scoring::ImplicitFastClashCheck:

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_

Detailed Description

Definition at line 36 of file ImplicitFastClashCheck.hh.

Constructor & Destructor Documentation

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

virtual

Automatically generated virtual destructor for class deriving directly from ReferenceCount.

Auto-generated virtual destructor

Definition at line 30 of file ImplicitFastClashCheck.cc.

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

Definition at line 49 of file ImplicitFastClashCheck.cc.

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

Definition at line 42 of file ImplicitFastClashCheck.cc.

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

Definition at line 57 of file ImplicitFastClashCheck.cc.

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

Definition at line 264 of file ImplicitFastClashCheck.cc.

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

Definition at line 224 of file ImplicitFastClashCheck.cc.

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

platform::uint protocols::scoring::ImplicitFastClashCheck::clash_count

(

numeric::xyzVector< core::Real > const &

pp)

const

Definition at line 148 of file ImplicitFastClashCheck.cc.

References core::sequence::end, and core::io::serialization::size().

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

Definition at line 242 of file ImplicitFastClashCheck.cc.

References core::kinematics::Stub::global2local().

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

Definition at line 259 of file ImplicitFastClashCheck.cc.

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

Definition at line 67 of file ImplicitFastClashCheck.cc.

References core::scoring::electron_density::square().

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

inline

Definition at line 117 of file ImplicitFastClashCheck.hh.

References points_.

Member Data Documentation

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

private

Definition at line 129 of file ImplicitFastClashCheck.hh.

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

private

Definition at line 133 of file ImplicitFastClashCheck.hh.

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

private

Definition at line 140 of file ImplicitFastClashCheck.hh.

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

private

Definition at line 135 of file ImplicitFastClashCheck.hh.

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

private

Definition at line 141 of file ImplicitFastClashCheck.hh.

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

private

Definition at line 131 of file ImplicitFastClashCheck.hh.

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

private

Definition at line 139 of file ImplicitFastClashCheck.hh.

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

private

Definition at line 137 of file ImplicitFastClashCheck.hh.

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

private

Definition at line 142 of file ImplicitFastClashCheck.hh.

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

private

Definition at line 137 of file ImplicitFastClashCheck.hh.

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

private

Definition at line 142 of file ImplicitFastClashCheck.hh.

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

private

Definition at line 125 of file ImplicitFastClashCheck.hh.

Referenced by size().

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

private

Definition at line 123 of file ImplicitFastClashCheck.hh.

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

private

Definition at line 127 of file ImplicitFastClashCheck.hh.

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

private

Definition at line 137 of file ImplicitFastClashCheck.hh.

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

private

Definition at line 142 of file ImplicitFastClashCheck.hh.

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

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