protocols::sic_dock Namespace Reference

Namespaces
	scores

Classes
struct	AtomIDHashFunction
class	BuriedPolarScore
class	CBScore
struct	CBScoreVisitor
class	ConstraintSetScore
struct	CorrectionVisitor
class	EdgeStandScore
class	HelixScore
class	JointScore
class	LinkerScore
class	NoPoseXYX_Func
class	RigidScore
class	Rose
class	SICFast
struct	Vec3
struct	XfoxmScore
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 Xform	Xform
typedef utility::vector1< Vec >	Vecs
typedef utility::vector1< Real >	Reals
typedef utility::vector1< Size >	Sizes
typedef numeric::Xforms	Xforms
typedef utility::vector1 < RigidScoreCOP >	Scores
typedef utility::pointer::shared_ptr < RigidScore >	RigidScoreOP
typedef utility::pointer::shared_ptr < RigidScore const >	RigidScoreCOP
typedef utility::pointer::shared_ptr < CBScore >	CBScoreOP
typedef utility::pointer::shared_ptr < CBScore const >	CBScoreCOP
typedef utility::pointer::shared_ptr < LinkerScore >	LinkerScoreOP
typedef utility::pointer::shared_ptr < LinkerScore const >	LinkerScoreCOP
typedef utility::pointer::shared_ptr < ConstraintSetScore >	ConstraintSetScoreOP
typedef utility::pointer::shared_ptr < ConstraintSetScore const >	ConstraintSetScoreCOP
typedef utility::pointer::shared_ptr < JointScore >	JointScoreOP
typedef utility::pointer::shared_ptr < JointScore const >	JointScoreCOP
typedef utility::pointer::shared_ptr < SICFast >	SICFastOP
typedef utility::pointer::shared_ptr < SICFast const >	SICFastCOP
typedef utility::vector1 < std::pair< platform::Size, Vec3 > >	TermInfo
typedef utility::vector1< Mat >	Mats
typedef utility::pointer::shared_ptr < xyzStripeHashPoseWithMeta >	xyzStripeHashPoseWithMetaOP
typedef utility::pointer::shared_ptr < xyzStripeHashPoseWithMeta const >	xyzStripeHashPoseWithMetaCOP

Functions
void	get_xform_stats (Xform const &sir, Xform 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)
Xform	vec3_to_stub (Vec3 const &v3)
Xform	vec3_to_stub (Xform 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 (Xform const &lower, Xform const &upper)
Size	count_linkers (Xform const &lower, Xform const &upper, protocols::loophash::LoopHashLibraryOP loop_hash_library, Sizes const &loopsizes, core::Size radius)
core::Size	dump_loophash_linkers (Xform const &lower, Xform const &upper, protocols::loophash::LoopHashLibraryOP loop_hash_library, Sizes const &loopsizes, Size radius, std::string const &outtag)
Real	linker_count2score (Size count)
platform::Size	count_linkers (Xform const &lower, Xform const &upper, protocols::loophash::LoopHashLibraryOP loop_hash_library, utility::vector1< platform::Size > const &loopsizes, platform::Size radius=0)
platform::Size	dump_loophash_linkers (Xform const &lower, Xform const &upper, protocols::loophash::LoopHashLibraryOP loop_hash_library, utility::vector1< platform::Size > const &loopsizes, platform::Size radius=0, std::string const &outtag="")
bool	read_biounit (string const &fname, Pose &pose, int const &max_res, bool const &DEBUG)
bool	read_biounit (string const &fname, Pose &pose, utility::vector1< Real > &bfactors, utility::vector1< Real > &occupancy, int const &max_res, bool const &DEBUG)
bool	read_biounit (string const &fname, Pose &pose, vector1< Real > &bfactors, vector1< Real > &occupancy, vector1< int > &pdbres, std::map< int, char > &pdbchain, int &nresmodel1, int const &max_res, bool const &DEBUG)
static thread_local basic::Tracer	TR ("protocols.sic_dock.RigidScore")
std::ostream &	operator<< (std::ostream &out, Vec3 v)
template<typename T >
T	CBScore_dist_score (T const &sqdist, T const &start, T const &stop)
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, Xform const &xform_to_struct2_start, vector1< Vec > const &pa, vector1< Real > const &radii, Vec const &ori, double const &clash_dis_sq, double const &mindis_approx)
static thread_local basic::Tracer	TR ("protocols.sic_dock.util")
Real	get_rg (core::pose::Pose const &pose)
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)
void	make_Cx (core::pose::Pose &pose, int N, numeric::xyzVector< core::Real > axis)
double	slide_into_contact_and_score (protocols::sic_dock::SICFast const &sic, protocols::sic_dock::RigidScore const &sfxn, Xform &xa, Xform const &xb, numeric::xyzVector< core::Real > const &ori, core::Real &score)
double	slide_into_contact_and_score_DEPRICATED (protocols::sic_dock::SICFast const &sic, protocols::sic_dock::RigidScore const &sfxn, core::kinematics::Stub &xa, core::kinematics::Stub const &xb, numeric::xyzVector< core::Real > const &ori, core::Real &score)
core::id::AtomID_Map< double >	cb_weight_map_from_pose (core::pose::Pose const &pose)
core::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)
vector1< numeric::xyzVector < core::Real > >	get_CB_Vecs_from_pose (core::pose::Pose const &pose)
vector1< numeric::xyzVector < core::Real > >	get_CB_Vecs_from_map (core::pose::Pose const &pose, core::id::AtomID_Map< core::Real > const &map)
vector1< core::Real >	cb_weights_from_pose (core::pose::Pose const &pose)
vector1< core::Real >	cb_weights_from_map (core::pose::Pose const &pose, core::id::AtomID_Map< core::Real > const &map)
vector1< core::Size >	range (core::Size beg, core::Size end)
int	flood_fill3D (int i, int j, int k, ObjexxFCL::FArray3D< double > &grid, double t)
bool	residue_is_floppy (core::pose::Pose const &pose, Size const ir, Real const ttrim_cut, Size const nfold)
void	auto_trim_floppy_termini (core::pose::Pose &pose, Real const ttrim_cut, Size const nfold)
void	dump_points_pdb (vector1< Vec > const &p, std::string fn)
void	dump_points_pdb (vector1< Vec > const &p, Vec t, std::string fn)
void	trans_pose (Pose &pose, Vec const &trans, Size start, Size end)
void	rot_pose (Pose &pose, Mat const &rot, Size start, Size end)
void	rot_pose (Pose &pose, Mat const &rot, Vec const &cen, Size start, Size end)
void	rot_pose (Pose &pose, Vec const &axis, Real const &ang, Size start, Size end)
void	rot_pose (Pose &pose, Vec const &axis, Real const &ang, Vec const &cen, Size start, Size end)
void	alignaxis (Pose &pose, Vec newaxis, Vec oldaxis, Vec cen)
numeric::xyzTransform< core::Real >	alignaxis_xform (numeric::xyzVector< core::Real > newaxis, numeric::xyzVector< core::Real > oldaxis, numeric::xyzVector< core::Real > cen)
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)
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)
Vec	center_of_geom (core::pose::Pose const &pose, Size str, Size end)
core::kinematics::Stub	getxform (core::conformation::Residue const &move_resi, core::conformation::Residue const &fixd_resi)
Real	brute_mindis (vector1< Vec > const &pa, vector1< Vec > const &pb, Vec const &ofst=Vec(0, 0, 0))
std::string	KMGT (double const &x, int const &w, int const &d)
Xform	multstubs (Xform const &a, Xform const &b)
Xform	invstub (Xform const &a)
void	dump_points_pdb (utility::vector1< numeric::xyzVector< core::Real > > const &p, std::string fn)
void	dump_points_pdb (utility::vector1< numeric::xyzVector< core::Real > > const &p, numeric::xyzVector< core::Real > t, std::string fn)
void	trans_pose (core::pose::Pose &pose, numeric::xyzVector< core::Real > const &trans, core::Size start=1, core::Size end=0)
void	rot_pose (core::pose::Pose &pose, numeric::xyzMatrix< core::Real > const &rot, core::Size start=1, core::Size end=0)
void	rot_pose (core::pose::Pose &pose, numeric::xyzMatrix< core::Real > const &rot, numeric::xyzVector< core::Real > const &cen, core::Size start=1, core::Size end=0)
void	rot_pose (core::pose::Pose &pose, numeric::xyzVector< core::Real > const &axis, core::Real const &ang, core::Size start=1, core::Size end=0)
void	rot_pose (core::pose::Pose &pose, numeric::xyzVector< core::Real > const &axis, core::Real const &ang, numeric::xyzVector< core::Real > const &cen, core::Size start=1, core::Size end=0)
void	alignaxis (core::pose::Pose &pose, numeric::xyzVector< core::Real > newaxis, numeric::xyzVector< core::Real > oldaxis, numeric::xyzVector< core::Real > cen=numeric::xyzVector< core::Real >(0, 0, 0))
numeric::xyzVector< core::Real >	projperp (numeric::xyzVector< core::Real > const &u, numeric::xyzVector< core::Real > const &v)
template<typename T >
T	sqr (T x)

Typedef Documentation

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

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

typedef utility::pointer::shared_ptr< ConstraintSetScore const > protocols::sic_dock::ConstraintSetScoreCOP

typedef utility::pointer::shared_ptr< ConstraintSetScore > protocols::sic_dock::ConstraintSetScoreOP

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

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

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

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

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

typedef utility::vector1<Mat> protocols::sic_dock::Mats

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

typedef core::Real protocols::sic_dock::Real

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

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

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

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

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

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

typedef core::Size protocols::sic_dock::Size

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

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

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

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

typedef Xform protocols::sic_dock::Xform

typedef numeric::Xforms protocols::sic_dock::Xforms

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

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

Function Documentation

void protocols::sic_dock::alignaxis	(	core::pose::Pose &	pose,
		numeric::xyzVector< core::Real >	newaxis,
		numeric::xyzVector< core::Real >	oldaxis,
		numeric::xyzVector< core::Real >	cen = numeric::xyzVector< core::Real >(0, 0, 0)
	)

void protocols::sic_dock::alignaxis	(	Pose &	pose,
		Vec	newaxis,
		Vec	oldaxis,
		Vec	cen
	)

References numeric::xyzVector< class >::cross(), numeric::xyzVector< class >::dot(), numeric::max(), numeric::min(), numeric::xyzVector< class >::normalize(), numeric::xyzVector< class >::normalized(), numeric::constants::f::pi, and rot_pose().

numeric::xyzTransform< core::Real > protocols::sic_dock::alignaxis_xform	(	numeric::xyzVector< core::Real >	newaxis,
		numeric::xyzVector< core::Real >	oldaxis,
		numeric::xyzVector< core::Real >	cen
	)

References numeric::xyzVector< class >::cross(), numeric::xyzVector< class >::dot(), numeric::max(), numeric::min(), numeric::xyzVector< class >::normalize(), numeric::xyzVector< class >::normalized(), numeric::constants::f::pi, and numeric::xyzTransform< class >::rot_deg().

void protocols::sic_dock::auto_trim_floppy_termini	(	core::pose::Pose &	pose,
		Real const	ttrim_cut,
		Size const	nfold
	)

References core::pose::Pose::conformation(), core::conformation::Conformation::delete_residue_slow(), core::pose::Pose::n_residue(), residue_is_floppy(), and TR().

Real protocols::sic_dock::brute_mindis	(	vector1< Vec > const &	pa,
		vector1< Vec > const &	pb,
		Vec const &	ofst = Vec(0,0,0)
	)

References min().

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

References numeric::min(), 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

)

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< core::Real > protocols::sic_dock::cb_weights_from_map	(	core::pose::Pose const &	pose,
		core::id::AtomID_Map< core::Real > const &	map
	)

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

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

(

core::pose::Pose const &

pose

)

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

template<typename T >

T protocols::sic_dock::CBScore_dist_score ( T const &  sqdist, T const &  start, T const &  stop  )

inline

References protocols::loops::start.

Referenced by protocols::sic_dock::scores::TrisBpyScore::score_extra(), and protocols::sic_dock::CBScoreVisitor::visit().

numeric::xyzVector< core::Real > protocols::sic_dock::center_of_geom	(	core::pose::Pose const &	pose,
		Size	str,
		Size	end
	)

References c, core::pose::Pose::n_residue(), and core::pose::Pose::xyz().

Referenced by get_rg().

core::Size protocols::sic_dock::count_CBs

(

core::pose::Pose const &

pose

)

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	(	Xform const &	lower,
		Xform const &	upper,
		protocols::loophash::LoopHashLibraryOP	loop_hash_library,
		utility::vector1< platform::Size > const &	loopsizes,
		platform::Size	radius = 0
	)

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

References get_leap_6dof(), core::kinematics::RT::get_translation(), and numeric::xyzVector< class >::length_squared().

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

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

inline

References protocols::loops::start.

platform::Size protocols::sic_dock::dump_loophash_linkers	(	Xform const &	lower,
		Xform const &	upper,
		protocols::loophash::LoopHashLibraryOP	loop_hash_library,
		utility::vector1< platform::Size > const &	loopsizes,
		platform::Size	radius = 0,
		std::string const &	outtag = ""
	)

core::Size protocols::sic_dock::dump_loophash_linkers	(	Xform const &	lower,
		Xform const &	upper,
		protocols::loophash::LoopHashLibraryOP	loop_hash_library,
		Sizes const &	loopsizes,
		Size	radius,
		std::string const &	outtag
	)

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(), get_leap_6dof(), get_leap_lower_stub(), protocols::loophash::LeapIndex::index, core::pose::Pose::n_residue(), protocols::loophash::LeapIndex::offset, omega, core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), core::pose::Pose::total_residue(), vec3_to_stub(), and xform_pose().

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

void protocols::sic_dock::dump_points_pdb	(	utility::vector1< numeric::xyzVector< core::Real > > const &	p,
		std::string	fn
	)

void protocols::sic_dock::dump_points_pdb	(	utility::vector1< numeric::xyzVector< core::Real > > const &	p,
		numeric::xyzVector< core::Real >	t,
		std::string	fn
	)

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

References F, I, x(), y(), and z().

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

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

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

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
	)

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

inline

References max(), and min().

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

utility::vector1< numeric::xyzVector< core::Real > > protocols::sic_dock::get_CB_Vecs_from_map	(	core::pose::Pose const &	pose,
		core::id::AtomID_Map< core::Real > const &	map
	)

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

utility::vector1< numeric::xyzVector< core::Real > > protocols::sic_dock::get_CB_Vecs_from_pose

(

core::pose::Pose const &

pose

)

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	(	Xform const &	lower,
		Xform const &	upper
	)

References core::kinematics::RT::get_rotation(), core::kinematics::RT::get_translation(), numeric::constants::d::pi, numeric::xyzVector< class >::x(), numeric::xyzVector< class >::y(), and numeric::xyzVector< class >::z().

Referenced by count_linkers(), and dump_loophash_linkers().

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

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
	)

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

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

core::Real protocols::sic_dock::get_rg

(

core::pose::Pose const &

pose

)

References core::conformation::Residue::aa(), core::chemical::aa_vrt, center_of_geom(), protocols::membrane::geometry::center_of_mass(), core::pose::Pose::n_residue(), core::conformation::Residue::nbr_atom_xyz(), and core::pose::Pose::residue().

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

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(), core::pose::Pose::residue(), and TR().

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
	)

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

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

References numeric::constants::d::pi, numeric::xyzMatrix< class >::transposed(), numeric::xyzVector< class >::x(), numeric::xyzMatrix< class >::xx(), numeric::xyzMatrix< class >::xy(), numeric::xyzMatrix< class >::xz(), numeric::xyzVector< class >::y(), numeric::xyzMatrix< class >::yx(), numeric::xyzVector< class >::z(), numeric::xyzMatrix< class >::zx(), numeric::xyzMatrix< class >::zy(), and numeric::xyzMatrix< class >::zz().

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

core::kinematics::Stub protocols::sic_dock::getxform	(	core::conformation::Residue const &	move_resi,
		core::conformation::Residue const &	fixd_resi
	)

References alignVectorSets(), core::kinematics::Stub::M, core::kinematics::Stub::v, and core::conformation::Residue::xyz().

Xform protocols::sic_dock::invstub ( Xform const &  a )

inline

References numeric::xyzMatrix< class >::transposed().

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

std::string protocols::sic_dock::KMGT	(	double const &	x,
		int const &	w,
		int const &	d
	)

References F.

platform::Real protocols::sic_dock::linker_count2score

(

Size

count

)

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

void protocols::sic_dock::make_Cx	(	core::pose::Pose &	pose,
		int	N,
		numeric::xyzVector< core::Real >	axis
	)

References core::pose::Pose::append_residue_by_bond(), core::pose::Pose::append_residue_by_jump(), core::conformation::Residue::is_ligand(), core::conformation::Residue::is_lower_terminus(), core::pose::Pose::n_residue(), core::pose::Pose::residue(), and rot_pose().

Xform protocols::sic_dock::multstubs ( Xform const &  a, Xform const &  b  )

inline

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

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

References 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(), 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
	)

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
	)

References count_CBs().

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

References count_CBs().

numeric::xyzVector<core::Real> protocols::sic_dock::projperp ( numeric::xyzVector< core::Real > const &  u, numeric::xyzVector< core::Real > const &  v  )

inline

References projection_matrix().

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

Referenced by protocols::helical_bundle::BackboneGridSampler::add_torsion_to_sample(), protocols::domain_assembly::AddAssemblyConstraints::apply(), protocols::environment::claims::CutBiasClaim::CutBiasClaim(), 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::abinitio::abscript::AbscriptMover::parse_stage_id(), 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(), protocols::noesy_assign::PeakAssignmentParameters::set_options_from_cmdline(), and protocols::membrane::SpinAroundPartnerMover::SpinAroundPartnerMover().

bool protocols::sic_dock::read_biounit	(	string const &	fname,
		Pose &	pose,
		int const &	max_res,
		bool const &	DEBUG
	)

Referenced by read_biounit().

bool protocols::sic_dock::read_biounit	(	string const &	fname,
		Pose &	pose,
		utility::vector1< Real > &	bfactors,
		utility::vector1< Real > &	occupancy,
		int const &	max_res,
		bool const &	DEBUG
	)

References read_biounit().

bool protocols::sic_dock::read_biounit	(	string const &	fname,
		Pose &	pose,
		vector1< Real > &	bfactors,
		vector1< Real > &	occupancy,
		vector1< int > &	pdbres,
		std::map< int, char > &	pdbchain,
		int &	nresmodel1,
		int const &	max_res,
		bool const &	DEBUG
	)

References core::pose::Pose::append_residue_by_bond(), core::pose::Pose::append_residue_by_jump(), cerr, core::pose::Pose::chain(), core::pose::Pose::conformation(), cout, core::conformation::Conformation::detect_disulfides(), core::pose::Pose::dump_pdb(), core::chemical::FA_STANDARD, utility::file_basename(), core::pose::Pose::n_residue(), pose_from_pdb(), and utility_exit_with_message.

double protocols::sic_dock::refine_mindis_with_xyzHash ( xyzStripeHashPose *  xh, Xform const &  xform_to_struct2_start, vector1< Vec > const &  pa, vector1< Real > const &  radii, Vec const &  ori, double const &  clash_dis_sq, double const &  mindis_approx  )

inline

References protocols::sic_dock::CorrectionVisitor::contacts, protocols::sic_dock::CorrectionVisitor::correction, numeric::xyzVector< class >::normalized(), rotation_matrix_degrees(), and numeric::xyzVector< class >::z().

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

bool protocols::sic_dock::residue_is_floppy	(	core::pose::Pose const &	pose,
		Size const	ir,
		Real const	ttrim_cut,
		Size const	nfold
	)

References numeric::xyzVector< class >::distance_squared(), core::pose::Pose::n_residue(), core::conformation::Residue::nheavyatoms(), core::pose::Pose::residue(), rotation_matrix_degrees(), and core::conformation::Residue::xyz().

Referenced by auto_trim_floppy_termini().

void protocols::sic_dock::rot_pose	(	core::pose::Pose &	pose,
		numeric::xyzMatrix< core::Real > const &	rot,
		core::Size	start = 1,
		core::Size	end = 0
	)

void protocols::sic_dock::rot_pose	(	core::pose::Pose &	pose,
		numeric::xyzMatrix< core::Real > const &	rot,
		numeric::xyzVector< core::Real > const &	cen,
		core::Size	start = 1,
		core::Size	end = 0
	)

void protocols::sic_dock::rot_pose	(	core::pose::Pose &	pose,
		numeric::xyzVector< core::Real > const &	axis,
		core::Real const &	ang,
		core::Size	start = 1,
		core::Size	end = 0
	)

void protocols::sic_dock::rot_pose	(	core::pose::Pose &	pose,
		numeric::xyzVector< core::Real > const &	axis,
		core::Real const &	ang,
		numeric::xyzVector< core::Real > const &	cen,
		core::Size	start = 1,
		core::Size	end = 0
	)

void protocols::sic_dock::rot_pose	(	Pose &	pose,
		Mat const &	rot,
		Size	start,
		Size	end
	)

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().

Referenced by alignaxis(), make_Cx(), and rot_pose().

void protocols::sic_dock::rot_pose	(	Pose &	pose,
		Mat const &	rot,
		Vec const &	cen,
		Size	start,
		Size	end
	)

References rot_pose(), and trans_pose().

void protocols::sic_dock::rot_pose	(	Pose &	pose,
		Vec const &	axis,
		Real const &	ang,
		Size	start,
		Size	end
	)

References rot_pose(), and rotation_matrix_degrees().

void protocols::sic_dock::rot_pose	(	Pose &	pose,
		Vec const &	axis,
		Real const &	ang,
		Vec const &	cen,
		Size	start,
		Size	end
	)

References rot_pose(), and rotation_matrix_degrees().

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

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

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

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

template<typename T >

T protocols::sic_dock::sqr ( T  x )

inline

static thread_local basic::Tracer protocols::sic_dock::TR ( "protocols.sic_dock.util"  )

static

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

static

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

void protocols::sic_dock::trans_pose	(	core::pose::Pose &	pose,
		numeric::xyzVector< core::Real > const &	trans,
		core::Size	start = 1,
		core::Size	end = 0
	)

void protocols::sic_dock::trans_pose	(	Pose &	pose,
		Vec const &	trans,
		Size	start,
		Size	end
	)

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().

Referenced by rot_pose().

Xform protocols::sic_dock::vec3_to_stub

(

Vec3 const &

v3

)

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

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

Xform protocols::sic_dock::vec3_to_stub	(	Xform const &	xform,
		Vec3 const &	v3
	)

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

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

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().

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

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
	)

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().

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

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().