protocols::sic_dock Namespace Reference

Classes
struct	XfoxmScore
struct	CBScoreVisitor
class	RigidScore
class	CBScore
class	LinkerScore
class	EdgeStandScore
class	HelixScore
class	BuriedPolarScore
class	JointScore
class	Rose
struct	CorrectionVisitor
class	SICFast
struct	Vec3
class	xyzStripeHashPose
class	xyzStripeHashPoseWithMeta

Typedefs
typedef numeric::xyzVector < platform::Real >	Vec
typedef numeric::xyzMatrix < platform::Real >	Mat
typedef core::Real	Real
typedef core::Size	Size
typedef core::pose::Pose	Pose
typedef core::kinematics::Stub	Stub
typedef utility::vector1< Vec >	Vecs
typedef utility::vector1< Real >	Reals
typedef utility::vector1< Size >	Sizes
typedef utility::vector1< Stub >	Stubs
typedef utility::vector1 < RigidScoreCOP >	Scores
typedef utility::pointer::owning_ptr < RigidScore >	RigidScoreOP
typedef utility::pointer::owning_ptr < RigidScore const >	RigidScoreCOP
typedef utility::pointer::owning_ptr < CBScore >	CBScoreOP
typedef utility::pointer::owning_ptr < CBScore const >	CBScoreCOP
typedef utility::pointer::owning_ptr < LinkerScore >	LinkerScoreOP
typedef utility::pointer::owning_ptr < LinkerScore const >	LinkerScoreCOP
typedef utility::pointer::owning_ptr < JointScore >	JointScoreOP
typedef utility::pointer::owning_ptr < JointScore const >	JointScoreCOP
typedef utility::pointer::owning_ptr < SICFast >	SICFastOP
typedef utility::pointer::owning_ptr < SICFast const >	SICFastCOP
typedef utility::vector1 < std::pair< platform::Size, Vec3 > >	TermInfo
typedef utility::pointer::owning_ptr < xyzStripeHashPose >	xyzStripeHashPoseOP
typedef utility::pointer::owning_ptr < xyzStripeHashPose const >	xyzStripeHashPoseCOP
typedef utility::pointer::owning_ptr < xyzStripeHashPoseWithMeta >	xyzStripeHashPoseWithMetaOP
typedef utility::pointer::owning_ptr < xyzStripeHashPoseWithMeta const >	xyzStripeHashPoseWithMetaCOP

Enumerations
enum	PoseCoordPickMode {   NBR, CA, CB, BB,   BNP, HVY, ALL }

Functions
void	get_xform_stats (core::kinematics::Stub const &sir, core::kinematics::Stub const &sjr, Real &dx, Real &dy, Real &dz, Real &ex, Real &ey, Real &ez)
Vec3	get_leap_lower_stub (core::pose::Pose const &pose, Size ir)
Vec3	get_leap_upper_stub (core::pose::Pose const &pose, Size ir)
core::kinematics::Stub	vec3_to_stub (Vec3 const &v3)
Stub	vec3_to_stub (core::kinematics::Stub const &xform, Vec3 const &v3)
void	get_termini_from_pose (core::pose::Pose const &pose, Size ir, TermInfo &lowers, TermInfo &uppers)
void	get_termini_from_pose (core::pose::Pose const &pose, TermInfo &lowers, TermInfo &uppers)
numeric::geometry::hashing::Real6	get_leap_6dof (Stub const &lower, Stub const &upper)
Size	count_linkers (Stub const &lower, Stub const &upper, protocols::loophash::LoopHashLibraryOP loop_hash_library, Sizes const &loopsizes, core::Size radius)
core::Size	dump_loophash_linkers (Stub const &lower, Stub const &upper, protocols::loophash::LoopHashLibraryOP loop_hash_library, Sizes const &loopsizes, Size radius)
Real	linker_count2score (Size count)
platform::Size	count_linkers (core::kinematics::Stub const &lower, core::kinematics::Stub const &upper, protocols::loophash::LoopHashLibraryOP loop_hash_library, utility::vector1< platform::Size > const &loopsizes, platform::Size radius=0)
platform::Size	dump_loophash_linkers (core::kinematics::Stub const &lower, core::kinematics::Stub const &upper, protocols::loophash::LoopHashLibraryOP loop_hash_library, utility::vector1< platform::Size > const &loopsizes, platform::Size radius=0)
static basic::Tracer	TR ("propocols.sic_dock.RigidScore")
Real	dist_score (Real const &sqdist, Real const &start, Real const &stop)
std::ostream &	operator<< (std::ostream &out, Vec3 v)
template<typename T >
T	sqr (T x)
void	dump_points_pdb (utility::vector1< Vec > const &p, std::string fn)
double	dist_score (double const &sqdist, double const &start, double const &stop)
bool	get_bounds_intersection (vector1< Vec > const &pb, vector1< Vec > const &pa, double &xmx, double &xmn, double &ymx, double &ymn)
void	fill_plane_hash (vector1< Vec > const &pb, vector1< Vec > const &pa, double const &xmx, double const &xmn, double const &ymx, double const &ymn, double const &BIN, ObjexxFCL::FArray2D< Vec > &ha, ObjexxFCL::FArray2D< Vec > &hb, int &xlb, int &ylb, int &xub, int &yub)
double	get_mindis_with_plane_hashes (int const &xlb, int const &ylb, int const &xub, int const &yub, ObjexxFCL::FArray2D< Vec > const &ha, ObjexxFCL::FArray2D< Vec > const &hb, double const &clashdis2)
double	refine_mindis_with_xyzHash (xyzStripeHashPose *xh, core::kinematics::Stub const &xform_to_struct2_start, vector1< Vec > const &pa, Vec const &ori, double const &clash_dis_sq, double const &mindis_approx)
int	neighbor_count (core::pose::Pose const &pose, int ires, double distance_threshold)
Real	cb_weight (core::pose::Pose const &pose, Size ires, Real distance_threshold)
double	slide_into_contact_and_score (protocols::sic_dock::SICFast const &sic, protocols::sic_dock::RigidScore const &sfxn, numeric::xyzTransform< core::Real > &xa, numeric::xyzTransform< core::Real > const &xb, numeric::xyzVector< platform::Real > const &ori, platform::Real &score)
double	slide_into_contact_and_score (protocols::sic_dock::SICFast const &sic, protocols::sic_dock::RigidScore const &sfxn, core::kinematics::Stub &xa, core::kinematics::Stub const &xb, numeric::xyzVector< platform::Real > const &ori, platform::Real &score)
core::id::AtomID_Map< double >	cb_weight_map_from_pose (core::pose::Pose const &pose)
utility::vector1< platform::Real >	cb_weights_from_pose (core::pose::Pose const &pose)
platform::Size	count_CBs (core::pose::Pose const &pose)
core::pose::Pose const &	pose_with_most_CBs (core::pose::Pose const &pose1, core::pose::Pose const &pose2)
bool	pose1_has_most_CBs (core::pose::Pose const &pose1, core::pose::Pose const &pose2)
utility::vector1 < numeric::xyzVector < platform::Real > >	get_CB_Vecs (core::pose::Pose const &pose)
void	xform_pose (core::pose::Pose &pose, core::kinematics::Stub const &s, Size sres, Size eres)
void	xform_pose_rev (core::pose::Pose &pose, core::kinematics::Stub const &s, Size sres, Size eres)
void	xform_pose (core::pose::Pose &pose, numeric::xyzTransform< core::Real > const &s, Size sres, Size eres)
void	xform_pose_rev (core::pose::Pose &pose, numeric::xyzTransform< core::Real > const &s)
utility::vector1< platform::Size >	range (platform::Size beg, platform::Size end)
int	flood_fill3D (int i, int j, int k, ObjexxFCL::FArray3D< double > &grid, double t)
core::kinematics::Stub	multstubs (core::kinematics::Stub const &a, core::kinematics::Stub const &b)
core::kinematics::Stub	invstub (core::kinematics::Stub const &a)

Typedef Documentation

typedef utility::pointer::owning_ptr< CBScore const > protocols::sic_dock::CBScoreCOP

Definition at line 24 of file RigidScore.fwd.hh.

typedef utility::pointer::owning_ptr< CBScore > protocols::sic_dock::CBScoreOP

Definition at line 22 of file RigidScore.fwd.hh.

typedef utility::pointer::owning_ptr< JointScore const > protocols::sic_dock::JointScoreCOP

Definition at line 44 of file RigidScore.fwd.hh.

typedef utility::pointer::owning_ptr< JointScore > protocols::sic_dock::JointScoreOP

Definition at line 42 of file RigidScore.fwd.hh.

typedef utility::pointer::owning_ptr< LinkerScore const > protocols::sic_dock::LinkerScoreCOP

Definition at line 28 of file RigidScore.fwd.hh.

typedef utility::pointer::owning_ptr< LinkerScore > protocols::sic_dock::LinkerScoreOP

Definition at line 26 of file RigidScore.fwd.hh.

typedef numeric::xyzMatrix< Real > protocols::sic_dock::Mat

Definition at line 27 of file designability_score.cc.

typedef core::pose::Pose protocols::sic_dock::Pose

Definition at line 32 of file loophash_util.cc.

typedef platform::Real protocols::sic_dock::Real

Definition at line 30 of file loophash_util.cc.

typedef utility::vector1< Real > protocols::sic_dock::Reals

Definition at line 37 of file loophash_util.cc.

typedef utility::pointer::owning_ptr< RigidScore const > protocols::sic_dock::RigidScoreCOP

Definition at line 20 of file RigidScore.fwd.hh.

typedef utility::pointer::owning_ptr< RigidScore > protocols::sic_dock::RigidScoreOP

Definition at line 18 of file RigidScore.fwd.hh.

typedef utility::vector1< RigidScoreCOP > protocols::sic_dock::Scores

Definition at line 40 of file loophash_util.cc.

typedef utility::pointer::owning_ptr< SICFast const > protocols::sic_dock::SICFastCOP

Definition at line 20 of file SICFast.fwd.hh.

typedef utility::pointer::owning_ptr< SICFast > protocols::sic_dock::SICFastOP

Definition at line 18 of file SICFast.fwd.hh.

typedef platform::Size protocols::sic_dock::Size

Definition at line 31 of file loophash_util.cc.

typedef utility::vector1< Size > protocols::sic_dock::Sizes

Definition at line 38 of file loophash_util.cc.

typedef core::kinematics::Stub protocols::sic_dock::Stub

Definition at line 33 of file loophash_util.cc.

typedef utility::vector1< Stub > protocols::sic_dock::Stubs

Definition at line 39 of file loophash_util.cc.

typedef utility::vector1<std::pair<platform::Size,Vec3> > protocols::sic_dock::TermInfo

Definition at line 20 of file types.hh.

typedef numeric::xyzVector< Real > protocols::sic_dock::Vec

Definition at line 26 of file designability_score.cc.

typedef utility::vector1< Vec > protocols::sic_dock::Vecs

Definition at line 36 of file loophash_util.cc.

typedef utility::pointer::owning_ptr< xyzStripeHashPose const > protocols::sic_dock::xyzStripeHashPoseCOP

Definition at line 20 of file xyzStripeHashPose.fwd.hh.

typedef utility::pointer::owning_ptr< xyzStripeHashPose > protocols::sic_dock::xyzStripeHashPoseOP

Definition at line 18 of file xyzStripeHashPose.fwd.hh.

typedef utility::pointer::owning_ptr< xyzStripeHashPoseWithMeta const > protocols::sic_dock::xyzStripeHashPoseWithMetaCOP

Definition at line 20 of file xyzStripeHashPoseWithMeta.fwd.hh.

typedef utility::pointer::owning_ptr< xyzStripeHashPoseWithMeta > protocols::sic_dock::xyzStripeHashPoseWithMetaOP

Definition at line 18 of file xyzStripeHashPoseWithMeta.fwd.hh.

Enumeration Type Documentation

enum protocols::sic_dock::PoseCoordPickMode

Enumerator
NBR
CA
CB
BB
BNP
HVY
ALL

Definition at line 22 of file types.hh.

Function Documentation

core::Real protocols::sic_dock::cb_weight	(	core::pose::Pose const &	pose,
		Size	ires,
		Real	distance_threshold
	)

Definition at line 53 of file util.cc.

References neighbor_count(), and core::pose::Pose::secstruct().

Referenced by cb_weight_map_from_pose(), and cb_weights_from_pose().

core::id::AtomID_Map< double > protocols::sic_dock::cb_weight_map_from_pose

(

core::pose::Pose const &

pose)

Definition at line 92 of file util.cc.

References core::conformation::Residue::atom_index(), cb_weight(), core::conformation::Residue::has(), core::pose::initialize_atomid_map(), core::pose::Pose::n_residue(), and core::pose::Pose::residue().

utility::vector1< platform::Real > protocols::sic_dock::cb_weights_from_pose

(

core::pose::Pose const &

pose)

Definition at line 106 of file util.cc.

References cb_weight(), core::conformation::Residue::has(), core::pose::Pose::n_residue(), and core::pose::Pose::residue().

Referenced by protocols::sic_dock::SICFast::init().

platform::Size protocols::sic_dock::count_CBs

(

core::pose::Pose const &

pose)

Definition at line 119 of file util.cc.

References core::conformation::Residue::has(), core::pose::Pose::n_residue(), and core::pose::Pose::residue().

Referenced by pose1_has_most_CBs(), and pose_with_most_CBs().

platform::Size protocols::sic_dock::count_linkers	(	core::kinematics::Stub const &	lower,
		core::kinematics::Stub const &	upper,
		protocols::loophash::LoopHashLibraryOP	loop_hash_library,
		utility::vector1< platform::Size > const &	loopsizes,
		platform::Size	radius = 0
	)

Size protocols::sic_dock::count_linkers	(	Stub const &	lower,
		Stub const &	upper,
		protocols::loophash::LoopHashLibraryOP	loop_hash_library,
		Sizes const &	loopsizes,
		core::Size	radius
	)

Definition at line 132 of file loophash_util.cc.

References get_leap_6dof(), and core::kinematics::RT::get_translation().

Referenced by protocols::sic_dock::LinkerScore::score().

Real protocols::sic_dock::dist_score ( Real const &  sqdist, Real const &  start, Real const &  stop  )

inline

Definition at line 53 of file RigidScore.cc.

References protocols::loops::start.

Referenced by core::scoring::hackaro::HackAroEnergy::eval_atom_derivative_aro_aro(), core::scoring::hackaro::HackAroEnergy::residue_pair_energy_aro_aro(), and protocols::sic_dock::CBScoreVisitor::visit().

double protocols::sic_dock::dist_score ( double const &  sqdist, double const &  start, double const &  stop  )

inline

Definition at line 55 of file SICFast.cc.

References protocols::loops::start.

platform::Size protocols::sic_dock::dump_loophash_linkers	(	core::kinematics::Stub const &	lower,
		core::kinematics::Stub const &	upper,
		protocols::loophash::LoopHashLibraryOP	loop_hash_library,
		utility::vector1< platform::Size > const &	loopsizes,
		platform::Size	radius = 0
	)

core::Size protocols::sic_dock::dump_loophash_linkers	(	Stub const &	lower,
		Stub const &	upper,
		protocols::loophash::LoopHashLibraryOP	loop_hash_library,
		Sizes const &	loopsizes,
		Size	radius
	)

Definition at line 156 of file loophash_util.cc.

References core::pose::Pose::append_residue_by_bond(), core::pose::Pose::append_residue_by_jump(), core::conformation::ResidueFactory::create_residue(), core::pose::Pose::dump_pdb(), protocols::loophash::BackboneDB::get_backbone_segment(), core::chemical::ChemicalManager::get_instance(), get_leap_6dof(), get_leap_lower_stub(), protocols::loophash::LeapIndex::index, core::pose::Pose::n_residue(), protocols::loophash::LeapIndex::offset, core::scoring::omega, protocols::swa::phi(), protocols::swa::psi(), core::chemical::ChemicalManager::residue_type_set(), core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), core::pose::Pose::total_residue(), vec3_to_stub(), xform_pose(), and xform_pose_rev().

Referenced by protocols::sic_dock::LinkerScore::score().

void protocols::sic_dock::dump_points_pdb	(	utility::vector1< Vec > const &	p,
		std::string	fn
	)

Definition at line 46 of file SICFast.cc.

void protocols::sic_dock::fill_plane_hash ( vector1< Vec > const &  pb, vector1< Vec > const &  pa, double const &  xmx, double const &  xmn, double const &  ymx, double const &  ymn, double const &  BIN, ObjexxFCL::FArray2D< Vec > &  ha, ObjexxFCL::FArray2D< Vec > &  hb, int &  xlb, int &  ylb, int &  xub, int &  yub  )

inline

Definition at line 167 of file SICFast.cc.

Referenced by protocols::sic_dock::SICFast::slide_into_contact().

int protocols::sic_dock::flood_fill3D	(	int	i,
		int	j,
		int	k,
		ObjexxFCL::FArray3D< double > &	grid,
		double	t
	)

Definition at line 205 of file util.cc.

References core::scoring::hbonds::t().

bool protocols::sic_dock::get_bounds_intersection ( vector1< Vec > const &  pb, vector1< Vec > const &  pa, double &  xmx, double &  xmn, double &  ymx, double &  ymn  )

inline

Definition at line 141 of file SICFast.cc.

Referenced by protocols::sic_dock::SICFast::slide_into_contact().

utility::vector1< numeric::xyzVector< platform::Real > > protocols::sic_dock::get_CB_Vecs

(

core::pose::Pose const &

pose)

Definition at line 145 of file util.cc.

References core::conformation::Residue::has(), core::pose::Pose::n_residue(), core::pose::Pose::residue(), and core::conformation::Residue::xyz().

numeric::geometry::hashing::Real6 protocols::sic_dock::get_leap_6dof	(	Stub const &	lower,
		Stub const &	upper
	)

Definition at line 114 of file loophash_util.cc.

References core::kinematics::RT::get_rotation(), and core::kinematics::RT::get_translation().

Referenced by count_linkers(), and dump_loophash_linkers().

Vec3 protocols::sic_dock::get_leap_lower_stub	(	core::pose::Pose const &	pose,
		Size	ir
	)

Definition at line 43 of file loophash_util.cc.

References protocols::sic_dock::Vec3::a, protocols::sic_dock::Vec3::b, protocols::sic_dock::Vec3::c, core::pose::Pose::residue(), and core::conformation::Residue::xyz().

Referenced by dump_loophash_linkers(), and get_termini_from_pose().

Vec3 protocols::sic_dock::get_leap_upper_stub	(	core::pose::Pose const &	pose,
		Size	ir
	)

Definition at line 55 of file loophash_util.cc.

References protocols::sic_dock::Vec3::a, protocols::sic_dock::Vec3::b, protocols::sic_dock::Vec3::c, core::pose::Pose::residue(), and core::conformation::Residue::xyz().

Referenced by get_termini_from_pose().

double protocols::sic_dock::get_mindis_with_plane_hashes ( int const &  xlb, int const &  ylb, int const &  xub, int const &  yub, ObjexxFCL::FArray2D< Vec > const &  ha, ObjexxFCL::FArray2D< Vec > const &  hb, double const &  clashdis2  )

inline

Definition at line 209 of file SICFast.cc.

Referenced by protocols::sic_dock::SICFast::slide_into_contact().

void protocols::sic_dock::get_termini_from_pose	(	core::pose::Pose const &	pose,
		Size	ir,
		TermInfo &	lowers,
		TermInfo &	uppers
	)

Definition at line 75 of file loophash_util.cc.

References get_leap_lower_stub(), get_leap_upper_stub(), core::conformation::Residue::is_lower_terminus(), core::conformation::Residue::is_protein(), core::conformation::Residue::is_upper_terminus(), core::pose::Pose::n_residue(), and core::pose::Pose::residue().

Referenced by get_termini_from_pose(), and protocols::sic_dock::LinkerScore::LinkerScore().

void protocols::sic_dock::get_termini_from_pose	(	core::pose::Pose const &	pose,
		TermInfo &	lowers,
		TermInfo &	uppers
	)

Definition at line 103 of file loophash_util.cc.

References get_termini_from_pose(), and core::pose::Pose::n_residue().

void protocols::sic_dock::get_xform_stats	(	core::kinematics::Stub const &	sir,
		core::kinematics::Stub const &	sjr,
		Real &	dx,
		Real &	dy,
		Real &	dz,
		Real &	ex,
		Real &	ey,
		Real &	ez
	)

Definition at line 30 of file designability_score.cc.

References core::kinematics::Stub::global2local(), core::kinematics::Stub::M, protocols::swa::phi(), protocols::swa::psi(), and core::kinematics::Stub::v.

Referenced by protocols::sic_dock::XfoxmScore::score().

core::kinematics::Stub protocols::sic_dock::invstub ( core::kinematics::Stub const &  a)

inline

Definition at line 114 of file util.hh.

References core::kinematics::Stub::M, and core::kinematics::Stub::v.

Referenced by protocols::sic_dock::CBScore::score().

platform::Real protocols::sic_dock::linker_count2score

(

Size

count)

Definition at line 234 of file loophash_util.cc.

Referenced by protocols::sic_dock::LinkerScore::score().

core::kinematics::Stub protocols::sic_dock::multstubs ( core::kinematics::Stub const &  a, core::kinematics::Stub const &  b  )

inline

Definition at line 111 of file util.hh.

References core::kinematics::Stub::M, and core::kinematics::Stub::v.

Referenced by protocols::sic_dock::CBScore::score().

int protocols::sic_dock::neighbor_count	(	core::pose::Pose const &	pose,
		int	ires,
		double	distance_threshold
	)

Definition at line 39 of file util.cc.

References core::kinematics::distance(), core::pose::Pose::n_residue(), and core::pose::Pose::residue().

Referenced by cb_weight(), protocols::toolbox::task_operations::ProteinCore::operator()(), protocols::optimize_weights::PNatAAOptEPositionData::print_score(), protocols::optimize_weights::PSSMOptEPositionData::print_score(), protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData::process_score(), protocols::forge::remodel::RemodelDesignMover::reduce_task(), protocols::qsar::scoring_grid::ChargeGrid::refresh(), core::scoring::nv::NVscore::residue_energy(), core::scoring::methods::PoissonBoltzmannEnergy::revamp_weight_by_burial(), protocols::optimize_weights::NestedEnergyTermPNatAAOptEPositionData::write_to_file(), and protocols::optimize_weights::PNatAAOptEPositionData::write_to_file().

std::ostream& protocols::sic_dock::operator<<	(	std::ostream &	out,
		Vec3	v
	)

Definition at line 65 of file RigidScore.cc.

References protocols::sic_dock::Vec3::a, protocols::sic_dock::Vec3::b, and protocols::sic_dock::Vec3::c.

bool protocols::sic_dock::pose1_has_most_CBs	(	core::pose::Pose const &	pose1,
		core::pose::Pose const &	pose2
	)

Definition at line 137 of file util.cc.

References count_CBs().

core::pose::Pose const & protocols::sic_dock::pose_with_most_CBs	(	core::pose::Pose const &	pose1,
		core::pose::Pose const &	pose2
	)

Definition at line 128 of file util.cc.

References count_CBs().

utility::vector1< platform::Size > protocols::sic_dock::range	(	platform::Size	beg,
		platform::Size	end
	)

Definition at line 199 of file util.cc.

References core::sequence::end.

Referenced by protocols::domain_assembly::AddAssemblyConstraints::apply(), core::scoring::methods::LK_SigmoidalFunc::dfunc(), core::scoring::methods::LK_SigmoidalFunc::func(), protocols::jobdist::BaseJobDistributor::get_next_random_range(), protocols::canonical_sampling::TemperingBase::init_from_options(), protocols::match::OccupiedSpaceHash::initialize(), protocols::match::Matcher::initialize_from_file(), protocols::loophash::LoopHashMap::lookup(), protocols::loophash::LoopHashMap::lookup_withkey(), protocols::loophash::LoopHashLibrary::merge(), protocols::fldsgn::MatchResidues::parse_my_tag(), protocols::loophash::LoopHashMap::radial_lookup(), protocols::loophash::BackboneDB::read_db(), protocols::loophash::LoopHashMap::read_db(), protocols::noesy_assign::PeakAssignmentParameters::register_options(), protocols::canonical_sampling::TemperingBase::register_options(), and protocols::noesy_assign::PeakAssignmentParameters::set_options_from_cmdline().

double protocols::sic_dock::refine_mindis_with_xyzHash ( xyzStripeHashPose *  xh, core::kinematics::Stub const &  xform_to_struct2_start, vector1< Vec > const &  pa, Vec const &  ori, double const &  clash_dis_sq, double const &  mindis_approx  )

inline

Definition at line 253 of file SICFast.cc.

References protocols::sic_dock::CorrectionVisitor::contacts, protocols::sic_dock::CorrectionVisitor::correction, core::kinematics::Stub::global2local(), and core::kinematics::Stub::M.

Referenced by protocols::sic_dock::SICFast::slide_into_contact().

double protocols::sic_dock::slide_into_contact_and_score	(	protocols::sic_dock::SICFast const &	sic,
		protocols::sic_dock::RigidScore const &	sfxn,
		numeric::xyzTransform< core::Real > &	xa,
		numeric::xyzTransform< core::Real > const &	xb,
		numeric::xyzVector< platform::Real > const &	ori,
		platform::Real &	score
	)

Definition at line 60 of file util.cc.

References core::scoring::sa, protocols::sic_dock::RigidScore::score(), and protocols::sic_dock::SICFast::slide_into_contact().

double protocols::sic_dock::slide_into_contact_and_score	(	protocols::sic_dock::SICFast const &	sic,
		protocols::sic_dock::RigidScore const &	sfxn,
		core::kinematics::Stub &	xa,
		core::kinematics::Stub const &	xb,
		numeric::xyzVector< platform::Real > const &	ori,
		platform::Real &	score
	)

Definition at line 77 of file util.cc.

References protocols::sic_dock::RigidScore::score(), protocols::sic_dock::SICFast::slide_into_contact(), and core::kinematics::Stub::v.

template<typename T >

T protocols::sic_dock::sqr ( T  x)

inline

Definition at line 43 of file SICFast.cc.

static basic::Tracer protocols::sic_dock::TR ( "propocols.sic_dock.RigidScore"  )

static

Referenced by protocols::sic_dock::LinkerScore::LinkerScore().

core::kinematics::Stub protocols::sic_dock::vec3_to_stub

(

Vec3 const &

v3)

Definition at line 66 of file loophash_util.cc.

References protocols::sic_dock::Vec3::a, protocols::sic_dock::Vec3::b, and protocols::sic_dock::Vec3::c.

Referenced by dump_loophash_linkers(), and protocols::sic_dock::LinkerScore::score().

core::kinematics::Stub protocols::sic_dock::vec3_to_stub	(	core::kinematics::Stub const &	xform,
		Vec3 const &	v3
	)

Definition at line 70 of file loophash_util.cc.

References protocols::sic_dock::Vec3::a, protocols::sic_dock::Vec3::b, protocols::sic_dock::Vec3::c, and core::kinematics::Stub::local2global().

void protocols::sic_dock::xform_pose	(	core::pose::Pose &	pose,
		core::kinematics::Stub const &	s,
		Size	sres,
		Size	eres
	)

Definition at line 158 of file util.cc.

References core::kinematics::Stub::local2global(), core::pose::Pose::n_residue(), core::chemical::ResidueType::natoms(), core::pose::Pose::residue_type(), core::pose::Pose::set_xyz(), and core::pose::Pose::xyz().

Referenced by dump_loophash_linkers(), and protocols::sic_dock::LinkerScore::score().

void protocols::sic_dock::xform_pose	(	core::pose::Pose &	pose,
		numeric::xyzTransform< core::Real > const &	s,
		Size	sres,
		Size	eres
	)

Definition at line 179 of file util.cc.

References core::pose::Pose::n_residue(), core::chemical::ResidueType::natoms(), core::pose::Pose::residue_type(), core::pose::Pose::set_xyz(), and core::pose::Pose::xyz().

void protocols::sic_dock::xform_pose_rev	(	core::pose::Pose &	pose,
		core::kinematics::Stub const &	s,
		Size	sres,
		Size	eres
	)

Definition at line 169 of file util.cc.

References core::kinematics::Stub::global2local(), core::pose::Pose::n_residue(), core::chemical::ResidueType::natoms(), core::pose::Pose::residue_type(), core::pose::Pose::set_xyz(), and core::pose::Pose::xyz().

Referenced by dump_loophash_linkers().

void protocols::sic_dock::xform_pose_rev	(	core::pose::Pose &	pose,
		numeric::xyzTransform< core::Real > const &	s
	)

Definition at line 188 of file util.cc.

References core::pose::Pose::n_residue(), core::chemical::ResidueType::natoms(), core::pose::Pose::residue_type(), core::pose::Pose::set_xyz(), and core::pose::Pose::xyz().